Fusion Propulsion Study

DTIC Science & Technology

1989-07-01

are established for particular missions. DESCRIPTION OF THE SCOPING CODE A fast-running FORTRAN code , TCT FOR, was written to perform the parameter...requirements; i.e., missions which require multi - stage , chemically propelled vehicles. Vehicle Sizing Algorithms The basic problem is the delivery of a...F04611-87-c-0092 77 - Ř ". -rd Z;PCc.e) 10 SOURCE OF FUNDING NUMBERS PROGRAM PROJECT " I WORK U"󈧕 FLEMENT NO NO. [ iQ ACCESSION NO 162302F 3058

A Three-Dimensional Unsteady CFD Model of Compressor Stability

NASA Technical Reports Server (NTRS)

Chima, Rodrick V.

2006-01-01

A three-dimensional unsteady CFD code called CSTALL has been developed and used to investigate compressor stability. The code solved the Euler equations through the entire annulus and all blade rows. Blade row turning, losses, and deviation were modeled using body force terms which required input data at stations between blade rows. The input data was calculated using a separate Navier-Stokes turbomachinery analysis code run at one operating point near stall, and was scaled to other operating points using overall characteristic maps. No information about the stalled characteristic was used. CSTALL was run in a 2-D throughflow mode for very fast calculations of operating maps and estimation of stall points. Calculated pressure ratio characteristics for NASA stage 35 agreed well with experimental data, and results with inlet radial distortion showed the expected loss of range. CSTALL was also run in a 3-D mode to investigate inlet circumferential distortion. Calculated operating maps for stage 35 with 120 degree distortion screens showed a loss in range and pressure rise. Unsteady calculations showed rotating stall with two part-span stall cells. The paper describes the body force formulation in detail, examines the computed results, and concludes with observations about the code.

A Fast Code for Jupiter Atmospheric Entry Analysis

NASA Technical Reports Server (NTRS)

Yauber, Michael E.; Wercinski, Paul; Yang, Lily; Chen, Yih-Kanq

1999-01-01

A fast code was developed to calculate the forebody heating environment and heat shielding that is required for Jupiter atmospheric entry probes. A carbon phenolic heat shield material was assumed and, since computational efficiency was a major goal, analytic expressions were used, primarily, to calculate the heating, ablation and the required insulation. The code was verified by comparison with flight measurements from the Galileo probe's entry. The calculation required 3.5 sec of CPU time on a work station, or three to four orders of magnitude less than for previous Jovian entry heat shields. The computed surface recessions from ablation were compared with the flight values at six body stations. The average, absolute, predicted difference in the recession was 13.7% too high. The forebody's mass loss was overpredicted by 5.3% and the heat shield mass was calculated to be 15% less than the probe's actual heat shield. However, the calculated heat shield mass did not include contingencies for the various uncertainties that must be considered in the design of probes. Therefore, the agreement with the Galileo probe's values was satisfactory in view of the code's fast running time and the methods' approximations.

Sensor Authentication: Embedded Processor Code

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

Svoboda, John

2012-09-25

Described is the c code running on the embedded Microchip 32bit PIC32MX575F256H located on the INL developed noise analysis circuit board. The code performs the following functions: Controls the noise analysis circuit board preamplifier voltage gains of 1, 10, 100, 000 Initializes the analog to digital conversion hardware, input channel selection, Fast Fourier Transform (FFT) function, USB communications interface, and internal memory allocations Initiates high resolution 4096 point 200 kHz data acquisition Computes complex 2048 point FFT and FFT magnitude. Services Host command set Transfers raw data to Host Transfers FFT result to host Communication error checking

Benchmark Simulations of the Thermal-Hydraulic Responses during EBR-II Inherent Safety Tests using SAM

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

Hu, Rui; Sumner, Tyler S.

2016-04-17

An advanced system analysis tool SAM is being developed for fast-running, improved-fidelity, and whole-plant transient analyses at Argonne National Laboratory under DOE-NE’s Nuclear Energy Advanced Modeling and Simulation (NEAMS) program. As an important part of code development, companion validation activities are being conducted to ensure the performance and validity of the SAM code. This paper presents the benchmark simulations of two EBR-II tests, SHRT-45R and BOP-302R, whose data are available through the support of DOE-NE’s Advanced Reactor Technology (ART) program. The code predictions of major primary coolant system parameter are compared with the test results. Additionally, the SAS4A/SASSYS-1 code simulationmore » results are also included for a code-to-code comparison.« less

A hybrid gyrokinetic ion and isothermal electron fluid code for astrophysical plasma

NASA Astrophysics Data System (ADS)

Kawazura, Y.; Barnes, M.

2018-05-01

This paper describes a new code for simulating astrophysical plasmas that solves a hybrid model composed of gyrokinetic ions (GKI) and an isothermal electron fluid (ITEF) Schekochihin et al. (2009) [9]. This model captures ion kinetic effects that are important near the ion gyro-radius scale while electron kinetic effects are ordered out by an electron-ion mass ratio expansion. The code is developed by incorporating the ITEF approximation into AstroGK, an Eulerian δf gyrokinetics code specialized to a slab geometry Numata et al. (2010) [41]. The new code treats the linear terms in the ITEF equations implicitly while the nonlinear terms are treated explicitly. We show linear and nonlinear benchmark tests to prove the validity and applicability of the simulation code. Since the fast electron timescale is eliminated by the mass ratio expansion, the Courant-Friedrichs-Lewy condition is much less restrictive than in full gyrokinetic codes; the present hybrid code runs ∼ 2√{mi /me } ∼ 100 times faster than AstroGK with a single ion species and kinetic electrons where mi /me is the ion-electron mass ratio. The improvement of the computational time makes it feasible to execute ion scale gyrokinetic simulations with a high velocity space resolution and to run multiple simulations to determine the dependence of turbulent dynamics on parameters such as electron-ion temperature ratio and plasma beta.

New technologies for advanced three-dimensional optimum shape design in aeronautics

NASA Astrophysics Data System (ADS)

Dervieux, Alain; Lanteri, Stéphane; Malé, Jean-Michel; Marco, Nathalie; Rostaing-Schmidt, Nicole; Stoufflet, Bruno

1999-05-01

The analysis of complex flows around realistic aircraft geometries is becoming more and more predictive. In order to obtain this result, the complexity of flow analysis codes has been constantly increasing, involving more refined fluid models and sophisticated numerical methods. These codes can only run on top computers, exhausting their memory and CPU capabilities. It is, therefore, difficult to introduce best analysis codes in a shape optimization loop: most previous works in the optimum shape design field used only simplified analysis codes. Moreover, as the most popular optimization methods are the gradient-based ones, the more complex the flow solver, the more difficult it is to compute the sensitivity code. However, emerging technologies are contributing to make such an ambitious project, of including a state-of-the-art flow analysis code into an optimisation loop, feasible. Among those technologies, there are three important issues that this paper wishes to address: shape parametrization, automated differentiation and parallel computing. Shape parametrization allows faster optimization by reducing the number of design variable; in this work, it relies on a hierarchical multilevel approach. The sensitivity code can be obtained using automated differentiation. The automated approach is based on software manipulation tools, which allow the differentiation to be quick and the resulting differentiated code to be rather fast and reliable. In addition, the parallel algorithms implemented in this work allow the resulting optimization software to run on increasingly larger geometries. Copyright

OCTGRAV: Sparse Octree Gravitational N-body Code on Graphics Processing Units

NASA Astrophysics Data System (ADS)

Gaburov, Evghenii; Bédorf, Jeroen; Portegies Zwart, Simon

2010-10-01

Octgrav is a very fast tree-code which runs on massively parallel Graphical Processing Units (GPU) with NVIDIA CUDA architecture. The algorithms are based on parallel-scan and sort methods. The tree-construction and calculation of multipole moments is carried out on the host CPU, while the force calculation which consists of tree walks and evaluation of interaction list is carried out on the GPU. In this way, a sustained performance of about 100GFLOP/s and data transfer rates of about 50GB/s is achieved. It takes about a second to compute forces on a million particles with an opening angle of heta approx 0.5. To test the performance and feasibility, we implemented the algorithms in CUDA in the form of a gravitational tree-code which completely runs on the GPU. The tree construction and traverse algorithms are portable to many-core devices which have support for CUDA or OpenCL programming languages. The gravitational tree-code outperforms tuned CPU code during the tree-construction and shows a performance improvement of more than a factor 20 overall, resulting in a processing rate of more than 2.8 million particles per second. The code has a convenient user interface and is freely available for use.

Program Processes Thermocouple Readings

NASA Technical Reports Server (NTRS)

Quave, Christine A.; Nail, William, III

1995-01-01

Digital Signal Processor for Thermocouples (DART) computer program implements precise and fast method of converting voltage to temperature for large-temperature-range thermocouple applications. Written using LabVIEW software. DART available only as object code for use on Macintosh II FX or higher-series computers running System 7.0 or later and IBM PC-series and compatible computers running Microsoft Windows 3.1. Macintosh version of DART (SSC-00032) requires LabVIEW 2.2.1 or 3.0 for execution. IBM PC version (SSC-00031) requires LabVIEW 3.0 for Windows 3.1. LabVIEW software product of National Instruments and not included with program.

Evaluation of nonlinear structural dynamic responses using a fast-running spring-mass formulation

NASA Astrophysics Data System (ADS)

Benjamin, A. S.; Altman, B. S.; Gruda, J. D.

In today's world, accurate finite-element simulations of large nonlinear systems may require meshes composed of hundreds of thousands of degrees of freedom. Even with today's fast computers and the promise of ever-faster ones in the future, central processing unit (CPU) expenditures for such problems could be measured in days. Many contemporary engineering problems, such as those found in risk assessment, probabilistic structural analysis, and structural design optimization, cannot tolerate the cost or turnaround time for such CPU-intensive analyses, because these applications require a large number of cases to be run with different inputs. For many risk assessment applications, analysts would prefer running times to be measurable in minutes. There is therefore a need for approximation methods which can solve such problems far more efficiently than the very detailed methods and yet maintain an acceptable degree of accuracy. For this purpose, we have been working on two methods of approximation: neural networks and spring-mass models. This paper presents our work and results to date for spring-mass modeling and analysis, since we are further along in this area than in the neural network formulation. It describes the physical and numerical models contained in a code we developed called STRESS, which stands for 'Spring-mass Transient Response Evaluation for structural Systems'. The paper also presents results for a demonstration problem, and compares these with results obtained for the same problem using PRONTO3D, a state-of-the-art finite element code which was also developed at Sandia.

Simulating Scenes In Outer Space

NASA Technical Reports Server (NTRS)

Callahan, John D.

1989-01-01

Multimission Interactive Picture Planner, MIP, computer program for scientifically accurate and fast, three-dimensional animation of scenes in deep space. Versatile, reasonably comprehensive, and portable, and runs on microcomputers. New techniques developed to perform rapidly calculations and transformations necessary to animate scenes in scientifically accurate three-dimensional space. Written in FORTRAN 77 code. Primarily designed to handle Voyager, Galileo, and Space Telescope. Adapted to handle other missions.

qtcm 0.1.2: A Python Implementation of the Neelin-Zeng Quasi-Equilibrium Tropical Circulation model

NASA Astrophysics Data System (ADS)

Lin, J. W.-B.

2008-10-01

Historically, climate models have been developed incrementally and in compiled languages like Fortran. While the use of legacy compiled languages results in fast, time-tested code, the resulting model is limited in its modularity and cannot take advantage of functionality available with modern computer languages. Here we describe an effort at using the open-source, object-oriented language Python to create more flexible climate models: the package qtcm, a Python implementation of the intermediate-level Neelin-Zeng Quasi-Equilibrium Tropical Circulation model (QTCM1) of the atmosphere. The qtcm package retains the core numerics of QTCM1, written in Fortran to optimize model performance, but uses Python structures and utilities to wrap the QTCM1 Fortran routines and manage model execution. The resulting "mixed language" modeling package allows order and choice of subroutine execution to be altered at run time, and model analysis and visualization to be integrated in interactively with model execution at run time. This flexibility facilitates more complex scientific analysis using less complex code than would be possible using traditional languages alone, and provides tools to transform the traditional "formulate hypothesis → write and test code → run model → analyze results" sequence into a feedback loop that can be executed automatically by the computer.

qtcm 0.1.2: a Python implementation of the Neelin-Zeng Quasi-Equilibrium Tropical Circulation Model

NASA Astrophysics Data System (ADS)

Lin, J. W.-B.

2009-02-01

Historically, climate models have been developed incrementally and in compiled languages like Fortran. While the use of legacy compiled languages results in fast, time-tested code, the resulting model is limited in its modularity and cannot take advantage of functionality available with modern computer languages. Here we describe an effort at using the open-source, object-oriented language Python to create more flexible climate models: the package qtcm, a Python implementation of the intermediate-level Neelin-Zeng Quasi-Equilibrium Tropical Circulation model (QTCM1) of the atmosphere. The qtcm package retains the core numerics of QTCM1, written in Fortran to optimize model performance, but uses Python structures and utilities to wrap the QTCM1 Fortran routines and manage model execution. The resulting "mixed language" modeling package allows order and choice of subroutine execution to be altered at run time, and model analysis and visualization to be integrated in interactively with model execution at run time. This flexibility facilitates more complex scientific analysis using less complex code than would be possible using traditional languages alone, and provides tools to transform the traditional "formulate hypothesis → write and test code → run model → analyze results" sequence into a feedback loop that can be executed automatically by the computer.

A Python Implementation of an Intermediate-Level Tropical Circulation Model and Implications for How Modeling Science is Done

NASA Astrophysics Data System (ADS)

Lin, J. W. B.

2015-12-01

Historically, climate models have been developed incrementally and in compiled languages like Fortran. While the use of legacy compiledlanguages results in fast, time-tested code, the resulting model is limited in its modularity and cannot take advantage of functionalityavailable with modern computer languages. Here we describe an effort at using the open-source, object-oriented language Pythonto create more flexible climate models: the package qtcm, a Python implementation of the intermediate-level Neelin-Zeng Quasi-Equilibrium Tropical Circulation model (QTCM1) of the atmosphere. The qtcm package retains the core numerics of QTCM1, written in Fortran, to optimize model performance but uses Python structures and utilities to wrap the QTCM1 Fortran routines and manage model execution. The resulting "mixed language" modeling package allows order and choice of subroutine execution to be altered at run time, and model analysis and visualization to be integrated in interactively with model execution at run time. This flexibility facilitates more complex scientific analysis using less complex code than would be possible using traditional languages alone and provides tools to transform the traditional "formulate hypothesis → write and test code → run model → analyze results" sequence into a feedback loop that can be executed automatically by the computer.

An Approach in Radiation Therapy Treatment Planning: A Fast, GPU-Based Monte Carlo Method.

PubMed

Karbalaee, Mojtaba; Shahbazi-Gahrouei, Daryoush; Tavakoli, Mohammad B

2017-01-01

An accurate and fast radiation dose calculation is essential for successful radiation radiotherapy. The aim of this study was to implement a new graphic processing unit (GPU) based radiation therapy treatment planning for accurate and fast dose calculation in radiotherapy centers. A program was written for parallel running based on GPU. The code validation was performed by EGSnrc/DOSXYZnrc. Moreover, a semi-automatic, rotary, asymmetric phantom was designed and produced using a bone, the lung, and the soft tissue equivalent materials. All measurements were performed using a Mapcheck dosimeter. The accuracy of the code was validated using the experimental data, which was obtained from the anthropomorphic phantom as the gold standard. The findings showed that, compared with those of DOSXYZnrc in the virtual phantom and for most of the voxels (>95%), <3% dose-difference or 3 mm distance-to-agreement (DTA) was found. Moreover, considering the anthropomorphic phantom, compared to the Mapcheck dose measurements, <5% dose-difference or 5 mm DTA was observed. Fast calculation speed and high accuracy of GPU-based Monte Carlo method in dose calculation may be useful in routine radiation therapy centers as the core and main component of a treatment planning verification system.

Creep force modelling for rail traction vehicles based on the Fastsim algorithm

NASA Astrophysics Data System (ADS)

Spiryagin, Maksym; Polach, Oldrich; Cole, Colin

2013-11-01

The evaluation of creep forces is a complex task and their calculation is a time-consuming process for multibody simulation (MBS). A methodology of creep forces modelling at large traction creepages has been proposed by Polach [Creep forces in simulations of traction vehicles running on adhesion limit. Wear. 2005;258:992-1000; Influence of locomotive tractive effort on the forces between wheel and rail. Veh Syst Dyn. 2001(Suppl);35:7-22] adapting his previously published algorithm [Polach O. A fast wheel-rail forces calculation computer code. Veh Syst Dyn. 1999(Suppl);33:728-739]. The most common method for creep force modelling used by software packages for MBS of running dynamics is the Fastsim algorithm by Kalker [A fast algorithm for the simplified theory of rolling contact. Veh Syst Dyn. 1982;11:1-13]. However, the Fastsim code has some limitations which do not allow modelling the creep force - creep characteristic in agreement with measurements for locomotives and other high-power traction vehicles, mainly for large traction creep at low-adhesion conditions. This paper describes a newly developed methodology based on a variable contact flexibility increasing with the ratio of the slip area to the area of adhesion. This variable contact flexibility is introduced in a modification of Kalker's code Fastsim by replacing the constant Kalker's reduction factor, widely used in MBS, by a variable reduction factor together with a slip-velocity-dependent friction coefficient decreasing with increasing global creepage. The proposed methodology is presented in this work and compared with measurements for different locomotives. The modification allows use of the well recognised Fastsim code for simulation of creep forces at large creepages in agreement with measurements without modifying the proven modelling methodology at small creepages.

Gravitational tree-code on graphics processing units: implementation in CUDA

NASA Astrophysics Data System (ADS)

Gaburov, Evghenii; Bédorf, Jeroen; Portegies Zwart, Simon

2010-05-01

We present a new very fast tree-code which runs on massively parallel Graphical Processing Units (GPU) with NVIDIA CUDA architecture. The tree-construction and calculation of multipole moments is carried out on the host CPU, while the force calculation which consists of tree walks and evaluation of interaction list is carried out on the GPU. In this way we achieve a sustained performance of about 100GFLOP/s and data transfer rates of about 50GB/s. It takes about a second to compute forces on a million particles with an opening angle of θ ≈ 0.5. The code has a convenient user interface and is freely available for use. http://castle.strw.leidenuniv.nl/software/octgrav.html

The Effect of Driver Rise-Time on Pinch Current and its Impact on Plasma Focus Performance and Neutron Yield

NASA Astrophysics Data System (ADS)

Sears, Jason; Schmidt, Andrea; Link, Anthony; Welch, Dale

2016-10-01

Experiments have suggested that dense plasma focus (DPF) neutron yield increases with faster drivers [Decker NIMP 1986]. Using the particle-in-cell code LSP [Schmidt PRL 2012], we reproduce this trend in a kJ DPF [Ellsworth 2014], and demonstrate how driver rise time is coupled to neutron output. We implement a 2-D model of the plasma focus including self-consistent circuit-driven boundary conditions. Driver capacitance and voltage are varied to modify the current rise time, and anode length is adjusted so that run-in coincides with the peak current. We observe during run down that magnetohydrodynamic (MHD) instabilities of the sheath shed blobs of plasma that remain in the inter-electrode gap during run in. This trailing plasma later acts as a low-inductance restrike path that shunts current from the pinch during maximum compression. While the MHD growth rate increases slightly with driver speed, the shorter anode of the fast driver allows fewer e-foldings and hence reduces the trailing mass between electrodes. As a result, the fast driver postpones parasitic restrikes and maintains peak current through the pinch during maximum compression. The fast driver pinch therefore achieves best simultaneity between its ion beam and peak target density, which maximizes neutron production. Prepared by LLNL under Contract DE-AC52-07NA27344.

Fast-Running Aeroelastic Code Based on Unsteady Linearized Aerodynamic Solver Developed

NASA Technical Reports Server (NTRS)

Reddy, T. S. R.; Bakhle, Milind A.; Keith, T., Jr.

2003-01-01

The NASA Glenn Research Center has been developing aeroelastic analyses for turbomachines for use by NASA and industry. An aeroelastic analysis consists of a structural dynamic model, an unsteady aerodynamic model, and a procedure to couple the two models. The structural models are well developed. Hence, most of the development for the aeroelastic analysis of turbomachines has involved adapting and using unsteady aerodynamic models. Two methods are used in developing unsteady aerodynamic analysis procedures for the flutter and forced response of turbomachines: (1) the time domain method and (2) the frequency domain method. Codes based on time domain methods require considerable computational time and, hence, cannot be used during the design process. Frequency domain methods eliminate the time dependence by assuming harmonic motion and, hence, require less computational time. Early frequency domain analyses methods neglected the important physics of steady loading on the analyses for simplicity. A fast-running unsteady aerodynamic code, LINFLUX, which includes steady loading and is based on the frequency domain method, has been modified for flutter and response calculations. LINFLUX, solves unsteady linearized Euler equations for calculating the unsteady aerodynamic forces on the blades, starting from a steady nonlinear aerodynamic solution. First, we obtained a steady aerodynamic solution for a given flow condition using the nonlinear unsteady aerodynamic code TURBO. A blade vibration analysis was done to determine the frequencies and mode shapes of the vibrating blades, and an interface code was used to convert the steady aerodynamic solution to a form required by LINFLUX. A preprocessor was used to interpolate the mode shapes from the structural dynamic mesh onto the computational dynamics mesh. Then, we used LINFLUX to calculate the unsteady aerodynamic forces for a given mode, frequency, and phase angle. A postprocessor read these unsteady pressures and calculated the generalized aerodynamic forces, eigenvalues, and response amplitudes. The eigenvalues determine the flutter frequency and damping. As a test case, the flutter of a helical fan was calculated with LINFLUX and compared with calculations from TURBO-AE, a nonlinear time domain code, and from ASTROP2, a code based on linear unsteady aerodynamics.

hybrid\\scriptsize{{MANTIS}}: a CPU-GPU Monte Carlo method for modeling indirect x-ray detectors with columnar scintillators

NASA Astrophysics Data System (ADS)

Sharma, Diksha; Badal, Andreu; Badano, Aldo

2012-04-01

The computational modeling of medical imaging systems often requires obtaining a large number of simulated images with low statistical uncertainty which translates into prohibitive computing times. We describe a novel hybrid approach for Monte Carlo simulations that maximizes utilization of CPUs and GPUs in modern workstations. We apply the method to the modeling of indirect x-ray detectors using a new and improved version of the code \\scriptsize{{MANTIS}}, an open source software tool used for the Monte Carlo simulations of indirect x-ray imagers. We first describe a GPU implementation of the physics and geometry models in fast\\scriptsize{{DETECT}}2 (the optical transport model) and a serial CPU version of the same code. We discuss its new features like on-the-fly column geometry and columnar crosstalk in relation to the \\scriptsize{{MANTIS}} code, and point out areas where our model provides more flexibility for the modeling of realistic columnar structures in large area detectors. Second, we modify \\scriptsize{{PENELOPE}} (the open source software package that handles the x-ray and electron transport in \\scriptsize{{MANTIS}}) to allow direct output of location and energy deposited during x-ray and electron interactions occurring within the scintillator. This information is then handled by optical transport routines in fast\\scriptsize{{DETECT}}2. A load balancer dynamically allocates optical transport showers to the GPU and CPU computing cores. Our hybrid\\scriptsize{{MANTIS}} approach achieves a significant speed-up factor of 627 when compared to \\scriptsize{{MANTIS}} and of 35 when compared to the same code running only in a CPU instead of a GPU. Using hybrid\\scriptsize{{MANTIS}}, we successfully hide hours of optical transport time by running it in parallel with the x-ray and electron transport, thus shifting the computational bottleneck from optical to x-ray transport. The new code requires much less memory than \\scriptsize{{MANTIS}} and, as a result, allows us to efficiently simulate large area detectors.

Incompressible SPH (ISPH) with fast Poisson solver on a GPU

NASA Astrophysics Data System (ADS)

Chow, Alex D.; Rogers, Benedict D.; Lind, Steven J.; Stansby, Peter K.

2018-05-01

This paper presents a fast incompressible SPH (ISPH) solver implemented to run entirely on a graphics processing unit (GPU) capable of simulating several millions of particles in three dimensions on a single GPU. The ISPH algorithm is implemented by converting the highly optimised open-source weakly-compressible SPH (WCSPH) code DualSPHysics to run ISPH on the GPU, combining it with the open-source linear algebra library ViennaCL for fast solutions of the pressure Poisson equation (PPE). Several challenges are addressed with this research: constructing a PPE matrix every timestep on the GPU for moving particles, optimising the limited GPU memory, and exploiting fast matrix solvers. The ISPH pressure projection algorithm is implemented as 4 separate stages, each with a particle sweep, including an algorithm for the population of the PPE matrix suitable for the GPU, and mixed precision storage methods. An accurate and robust ISPH boundary condition ideal for parallel processing is also established by adapting an existing WCSPH boundary condition for ISPH. A variety of validation cases are presented: an impulsively started plate, incompressible flow around a moving square in a box, and dambreaks (2-D and 3-D) which demonstrate the accuracy, flexibility, and speed of the methodology. Fragmentation of the free surface is shown to influence the performance of matrix preconditioners and therefore the PPE matrix solution time. The Jacobi preconditioner demonstrates robustness and reliability in the presence of fragmented flows. For a dambreak simulation, GPU speed ups demonstrate up to 10-18 times and 1.1-4.5 times compared to single-threaded and 16-threaded CPU run times respectively.

Efficient Helicopter Aerodynamic and Aeroacoustic Predictions on Parallel Computers

NASA Technical Reports Server (NTRS)

Wissink, Andrew M.; Lyrintzis, Anastasios S.; Strawn, Roger C.; Oliker, Leonid; Biswas, Rupak

1996-01-01

This paper presents parallel implementations of two codes used in a combined CFD/Kirchhoff methodology to predict the aerodynamics and aeroacoustics properties of helicopters. The rotorcraft Navier-Stokes code, TURNS, computes the aerodynamic flowfield near the helicopter blades and the Kirchhoff acoustics code computes the noise in the far field, using the TURNS solution as input. The overall parallel strategy adds MPI message passing calls to the existing serial codes to allow for communication between processors. As a result, the total code modifications required for parallel execution are relatively small. The biggest bottleneck in running the TURNS code in parallel comes from the LU-SGS algorithm that solves the implicit system of equations. We use a new hybrid domain decomposition implementation of LU-SGS to obtain good parallel performance on the SP-2. TURNS demonstrates excellent parallel speedups for quasi-steady and unsteady three-dimensional calculations of a helicopter blade in forward flight. The execution rate attained by the code on 114 processors is six times faster than the same cases run on one processor of the Cray C-90. The parallel Kirchhoff code also shows excellent parallel speedups and fast execution rates. As a performance demonstration, unsteady acoustic pressures are computed at 1886 far-field observer locations for a sample acoustics problem. The calculation requires over two hundred hours of CPU time on one C-90 processor but takes only a few hours on 80 processors of the SP2. The resultant far-field acoustic field is analyzed with state of-the-art audio and video rendering of the propagating acoustic signals.

a Virtual Trip to the Schwarzschild-De Sitter Black Hole

NASA Astrophysics Data System (ADS)

Bakala, Pavel; Hledík, Stanislav; Stuchlík, Zdenĕk; Truparová, Kamila; Čermák, Petr

2008-09-01

We developed realistic fully general relativistic computer code for simulation of optical projection in a strong, spherically symmetric gravitational field. Standard theoretical analysis of optical projection for an observer in the vicinity of a Schwarzschild black hole is extended to black hole spacetimes with a repulsive cosmological constant, i.e, Schwarzschild-de Sitter (SdS) spacetimes. Influence of the cosmological constant is investigated for static observers and observers radially free-falling from static radius. Simulation includes effects of gravitational lensing, multiple images, Doppler and gravitational frequency shift, as well as the amplification of intensity. The code generates images of static observers sky and a movie simulations for radially free-falling observers. Techniques of parallel programming are applied to get high performance and fast run of the simulation code.

Fast data preprocessing with Graphics Processing Units for inverse problem solving in light-scattering measurements

NASA Astrophysics Data System (ADS)

Derkachov, G.; Jakubczyk, T.; Jakubczyk, D.; Archer, J.; Woźniak, M.

2017-07-01

Utilising Compute Unified Device Architecture (CUDA) platform for Graphics Processing Units (GPUs) enables significant reduction of computation time at a moderate cost, by means of parallel computing. In the paper [Jakubczyk et al., Opto-Electron. Rev., 2016] we reported using GPU for Mie scattering inverse problem solving (up to 800-fold speed-up). Here we report the development of two subroutines utilising GPU at data preprocessing stages for the inversion procedure: (i) A subroutine, based on ray tracing, for finding spherical aberration correction function. (ii) A subroutine performing the conversion of an image to a 1D distribution of light intensity versus azimuth angle (i.e. scattering diagram), fed from a movie-reading CPU subroutine running in parallel. All subroutines are incorporated in PikeReader application, which we make available on GitHub repository. PikeReader returns a sequence of intensity distributions versus a common azimuth angle vector, corresponding to the recorded movie. We obtained an overall ∼ 400 -fold speed-up of calculations at data preprocessing stages using CUDA codes running on GPU in comparison to single thread MATLAB-only code running on CPU.

Predictions of Supersonic Jet Mixing and Shock-Associated Noise Compared With Measured Far-Field Data

NASA Technical Reports Server (NTRS)

Dahl, Milo D.

2010-01-01

Codes for predicting supersonic jet mixing and broadband shock-associated noise were assessed using a database containing noise measurements of a jet issuing from a convergent nozzle. Two types of codes were used to make predictions. Fast running codes containing empirical models were used to compute both the mixing noise component and the shock-associated noise component of the jet noise spectrum. One Reynolds-averaged, Navier-Stokes-based code was used to compute only the shock-associated noise. To enable the comparisons of the predicted component spectra with data, the measured total jet noise spectra were separated into mixing noise and shock-associated noise components. Comparisons were made for 1/3-octave spectra and some power spectral densities using data from jets operating at 24 conditions covering essentially 6 fully expanded Mach numbers with 4 total temperature ratios.

Fast and Sensitive Alignment of Microbial Whole Genome Sequencing Reads to Large Sequence Datasets on a Desktop PC: Application to Metagenomic Datasets and Pathogen Identification

PubMed Central

2014-01-01

Next generation sequencing (NGS) of metagenomic samples is becoming a standard approach to detect individual species or pathogenic strains of microorganisms. Computer programs used in the NGS community have to balance between speed and sensitivity and as a result, species or strain level identification is often inaccurate and low abundance pathogens can sometimes be missed. We have developed Taxoner, an open source, taxon assignment pipeline that includes a fast aligner (e.g. Bowtie2) and a comprehensive DNA sequence database. We tested the program on simulated datasets as well as experimental data from Illumina, IonTorrent, and Roche 454 sequencing platforms. We found that Taxoner performs as well as, and often better than BLAST, but requires two orders of magnitude less running time meaning that it can be run on desktop or laptop computers. Taxoner is slower than the approaches that use small marker databases but is more sensitive due the comprehensive reference database. In addition, it can be easily tuned to specific applications using small tailored databases. When applied to metagenomic datasets, Taxoner can provide a functional summary of the genes mapped and can provide strain level identification. Taxoner is written in C for Linux operating systems. The code and documentation are available for research applications at http://code.google.com/p/taxoner. PMID:25077800

Online and Offline Pattern Recognition in PANDA

NASA Astrophysics Data System (ADS)

Boca, Gianluigi

2016-11-01

PANDA is one of the four experiments that will run at the new facility FAIR that is being built in Darmstadt, Germany. It is a fixed target experiment: a beam of antiprotons collides on a jet proton target (the maximum center of mass energy is 5.46 GeV). The interaction rate at the startup will be 2MHz with the goal of reaching 20MHz at full luminosity. The beam of antiprotons will be essentially continuous. PANDA will have NO hardware trigger but only a software trigger, to allow for maximum flexibility in the physics program. All those characteristics are severe challenges for the reconstruction code that 1) must be fast, since it has to be validated up to 20MHz interaction rate; 2) must be able to reject fake tracks caused by the remnant hits, belonging to previous or later events in some slow detectors, for example the straw tubes in the central region. The Pattern Recognition (PR) of PANDA will have to run both online to achieve a first fast selection, and offline, at lower rate, for a more refined selection. In PANDA the PR code is continuously evolving; this contribution shows the present status. I will give an overview of three examples of PR following different strategies and/or implemented on different hardware (FPGA, GPUs, CPUs) and, when available, I will report the performances.

Fast and sensitive alignment of microbial whole genome sequencing reads to large sequence datasets on a desktop PC: application to metagenomic datasets and pathogen identification.

PubMed

Pongor, Lőrinc S; Vera, Roberto; Ligeti, Balázs

2014-01-01

Next generation sequencing (NGS) of metagenomic samples is becoming a standard approach to detect individual species or pathogenic strains of microorganisms. Computer programs used in the NGS community have to balance between speed and sensitivity and as a result, species or strain level identification is often inaccurate and low abundance pathogens can sometimes be missed. We have developed Taxoner, an open source, taxon assignment pipeline that includes a fast aligner (e.g. Bowtie2) and a comprehensive DNA sequence database. We tested the program on simulated datasets as well as experimental data from Illumina, IonTorrent, and Roche 454 sequencing platforms. We found that Taxoner performs as well as, and often better than BLAST, but requires two orders of magnitude less running time meaning that it can be run on desktop or laptop computers. Taxoner is slower than the approaches that use small marker databases but is more sensitive due the comprehensive reference database. In addition, it can be easily tuned to specific applications using small tailored databases. When applied to metagenomic datasets, Taxoner can provide a functional summary of the genes mapped and can provide strain level identification. Taxoner is written in C for Linux operating systems. The code and documentation are available for research applications at http://code.google.com/p/taxoner.

FQC Dashboard: integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool.

PubMed

Brown, Joseph; Pirrung, Meg; McCue, Lee Ann

2017-06-09

FQC is software that facilitates quality control of FASTQ files by carrying out a QC protocol using FastQC, parsing results, and aggregating quality metrics into an interactive dashboard designed to richly summarize individual sequencing runs. The dashboard groups samples in dropdowns for navigation among the data sets, utilizes human-readable configuration files to manipulate the pages and tabs, and is extensible with CSV data. FQC is implemented in Python 3 and Javascript, and is maintained under an MIT license. Documentation and source code is available at: https://github.com/pnnl/fqc . joseph.brown@pnnl.gov. © The Author(s) 2017. Published by Oxford University Press.

RAPTOR. I. Time-dependent radiative transfer in arbitrary spacetimes

NASA Astrophysics Data System (ADS)

Bronzwaer, T.; Davelaar, J.; Younsi, Z.; Mościbrodzka, M.; Falcke, H.; Kramer, M.; Rezzolla, L.

2018-05-01

Context. Observational efforts to image the immediate environment of a black hole at the scale of the event horizon benefit from the development of efficient imaging codes that are capable of producing synthetic data, which may be compared with observational data. Aims: We aim to present RAPTOR, a new public code that produces accurate images, animations, and spectra of relativistic plasmas in strong gravity by numerically integrating the equations of motion of light rays and performing time-dependent radiative transfer calculations along the rays. The code is compatible with any analytical or numerical spacetime. It is hardware-agnostic and may be compiled and run both on GPUs and CPUs. Methods: We describe the algorithms used in RAPTOR and test the code's performance. We have performed a detailed comparison of RAPTOR output with that of other radiative-transfer codes and demonstrate convergence of the results. We then applied RAPTOR to study accretion models of supermassive black holes, performing time-dependent radiative transfer through general relativistic magneto-hydrodynamical (GRMHD) simulations and investigating the expected observational differences between the so-called fast-light and slow-light paradigms. Results: Using RAPTOR to produce synthetic images and light curves of a GRMHD model of an accreting black hole, we find that the relative difference between fast-light and slow-light light curves is less than 5%. Using two distinct radiative-transfer codes to process the same data, we find integrated flux densities with a relative difference less than 0.01%. Conclusions: For two-dimensional GRMHD models, such as those examined in this paper, the fast-light approximation suffices as long as errors of a few percent are acceptable. The convergence of the results of two different codes demonstrates that they are, at a minimum, consistent. The public version of RAPTOR is available at the following URL: http://https://github.com/tbronzwaer/raptor

The relationship between gamma frequency and running speed differs for slow and fast gamma rhythms in freely behaving rats

PubMed Central

Zheng, Chenguang; Bieri, Kevin Wood; Trettel, Sean Gregory; Colgin, Laura Lee

2015-01-01

In hippocampal area CA1 of rats, the frequency of gamma activity has been shown to increase with running speed (Ahmed and Mehta, 2012). This finding suggests that different gamma frequencies simply allow for different timings of transitions across cell assemblies at varying running speeds, rather than serving unique functions. However, accumulating evidence supports the conclusion that slow (~25–55 Hz) and fast (~60–100 Hz) gamma are distinct network states with different functions. If slow and fast gamma constitute distinct network states, then it is possible that slow and fast gamma frequencies are differentially affected by running speed. In this study, we tested this hypothesis and found that slow and fast gamma frequencies change differently as a function of running speed in hippocampal areas CA1 and CA3, and in the superficial layers of the medial entorhinal cortex (MEC). Fast gamma frequencies increased with increasing running speed in all three areas. Slow gamma frequencies changed significantly less across different speeds. Furthermore, at high running speeds, CA3 firing rates were low, and MEC firing rates were high, suggesting that CA1 transitions from CA3 inputs to MEC inputs as running speed increases. These results support the hypothesis that slow and fast gamma reflect functionally distinct states in the hippocampal network, with fast gamma driven by MEC at high running speeds and slow gamma driven by CA3 at low running speeds. PMID:25601003

Centrifugal and Axial Pump Design and Off-Design Performance Prediction

NASA Technical Reports Server (NTRS)

Veres, Joseph P.

1995-01-01

A meanline pump-flow modeling method has been developed to provide a fast capability for modeling pumps of cryogenic rocket engines. Based on this method, a meanline pump-flow code PUMPA was written that can predict the performance of pumps at off-design operating conditions, given the loss of the diffusion system at the design point. The design-point rotor efficiency and slip factors are obtained from empirical correlations to rotor-specific speed and geometry. The pump code can model axial, inducer, mixed-flow, and centrifugal pumps and can model multistage pumps in series. The rapid input setup and computer run time for this meanline pump flow code make it an effective analysis and conceptual design tool. The map-generation capabilities of the code provide the information needed for interfacing with a rocket engine system modeling code. The off-design and multistage modeling capabilities of PUMPA permit the user to do parametric design space exploration of candidate pump configurations and to provide head-flow maps for engine system evaluation.

Fast simulation tool for ultraviolet radiation at the earth's surface

NASA Astrophysics Data System (ADS)

Engelsen, Ola; Kylling, Arve

2005-04-01

FastRT is a fast, yet accurate, UV simulation tool that computes downward surface UV doses, UV indices, and irradiances in the spectral range 290 to 400 nm with a resolution as small as 0.05 nm. It computes a full UV spectrum within a few milliseconds on a standard PC, and enables the user to convolve the spectrum with user-defined and built-in spectral response functions including the International Commission on Illumination (CIE) erythemal response function used for UV index calculations. The program accounts for the main radiative input parameters, i.e., instrumental characteristics, solar zenith angle, ozone column, aerosol loading, clouds, surface albedo, and surface altitude. FastRT is based on look-up tables of carefully selected entries of atmospheric transmittances and spherical albedos, and exploits the smoothness of these quantities with respect to atmospheric, surface, geometrical, and spectral parameters. An interactive site, http://nadir.nilu.no/~olaeng/fastrt/fastrt.html, enables the public to run the FastRT program with most input options. This page also contains updated information about FastRT and links to freely downloadable source codes and binaries.

Modelling the phase curve and occultation of WASP-43b with SPIDERMAN

NASA Astrophysics Data System (ADS)

Louden, Tom

2017-06-01

Presenting SPIDERMAN, a fast code for calculating exoplanet phase curves and secondary eclipses with arbitrary two dimensional surface brightness distributions. SPIDERMAN uses an exact geometric algorithm to calculate the area of sub-regions of the planet that are occulted by the star, with no loss in numerical precision. The speed of this calculation makes it possible to run MCMCs to marginalise effectively over the underlying parameters controlling the brightness distribution of exoplanets. The code is fully open source and available over Github. We apply the code to the phase curve of WASP-43b using an analytical surface brightness distribution, and find an excellent fit to the data. We are able to place direct constraints on the physics of heat transport in the atmosphere, such as the ratio between advective and radiative timescales at different altitudes.

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.

The Modeling of Advanced BWR Fuel Designs with the NRC Fuel Depletion Codes PARCS/PATHS

DOE PAGES

Ward, Andrew; Downar, Thomas J.; Xu, Y.; ...

2015-04-22

The PATHS (PARCS Advanced Thermal Hydraulic Solver) code was developed at the University of Michigan in support of U.S. Nuclear Regulatory Commission research to solve the steady-state, two-phase, thermal-hydraulic equations for a boiling water reactor (BWR) and to provide thermal-hydraulic feedback for BWR depletion calculations with the neutronics code PARCS (Purdue Advanced Reactor Core Simulator). The simplified solution methodology, including a three-equation drift flux formulation and an optimized iteration scheme, yields very fast run times in comparison to conventional thermal-hydraulic systems codes used in the industry, while still retaining sufficient accuracy for applications such as BWR depletion calculations. Lastly, themore » capability to model advanced BWR fuel designs with part-length fuel rods and heterogeneous axial channel flow geometry has been implemented in PATHS, and the code has been validated against previously benchmarked advanced core simulators as well as BWR plant and experimental data. We describe the modifications to the codes and the results of the validation in this paper.« less

Parallel Index and Query for Large Scale Data Analysis

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

Chou, Jerry; Wu, Kesheng; Ruebel, Oliver

2011-07-18

Modern scientific datasets present numerous data management and analysis challenges. State-of-the-art index and query technologies are critical for facilitating interactive exploration of large datasets, but numerous challenges remain in terms of designing a system for process- ing general scientific datasets. The system needs to be able to run on distributed multi-core platforms, efficiently utilize underlying I/O infrastructure, and scale to massive datasets. We present FastQuery, a novel software framework that address these challenges. FastQuery utilizes a state-of-the-art index and query technology (FastBit) and is designed to process mas- sive datasets on modern supercomputing platforms. We apply FastQuery to processing ofmore » a massive 50TB dataset generated by a large scale accelerator modeling code. We demonstrate the scalability of the tool to 11,520 cores. Motivated by the scientific need to search for inter- esting particles in this dataset, we use our framework to reduce search time from hours to tens of seconds.« less

TRANSURANUS: a fuel rod analysis code ready for use

NASA Astrophysics Data System (ADS)

Lassmann, K.

1992-06-01

TRANSURANUS is a computer program for the thermal and mechanical analysis of fuel rods in nuclear reactors and was developed at the European Institute for Transuranium Elements (TUI). The TRANSURANUS code consists of a clearly defined mechanical-mathematical framework into which physical models can easily be incorporated. Besides its flexibility for different fuel rod designs the TRANSURANUS code can deal with very different situations, as given for instance in an experiment, under normal, off-normal and accident conditions. The time scale of the problems to be treated may range from milliseconds to years. The code has a comprehensive material data bank for oxide, mixed oxide, carbide and nitride fuels, Zircaloy and steel claddings and different coolants. During its development great effort was spent on obtaining an extremely flexible tool which is easy to handle, exhibiting very fast running times. The total development effort is approximately 40 man-years. In recent years the interest to use this code grew and the code is in use in several organisations, both research and private industry. The code is now available to all interested parties. The paper outlines the main features and capabilities of the TRANSURANUS code, its validation and treats also some practical aspects.

Investigation of HZETRN 2010 as a Tool for Single Event Effect Qualification of Avionics Systems

NASA Technical Reports Server (NTRS)

Rojdev, Kristina; Koontz, Steve; Atwell, William; Boeder, Paul

2014-01-01

NASA's future missions are focused on long-duration deep space missions for human exploration which offers no options for a quick emergency return to Earth. The combination of long mission duration with no quick emergency return option leads to unprecedented spacecraft system safety and reliability requirements. It is important that spacecraft avionics systems for human deep space missions are not susceptible to Single Event Effect (SEE) failures caused by space radiation (primarily the continuous galactic cosmic ray background and the occasional solar particle event) interactions with electronic components and systems. SEE effects are typically managed during the design, development, and test (DD&T) phase of spacecraft development by using heritage hardware (if possible) and through extensive component level testing, followed by system level failure analysis tasks that are both time consuming and costly. The ultimate product of the SEE DD&T program is a prediction of spacecraft avionics reliability in the flight environment produced using various nuclear reaction and transport codes in combination with the component and subsystem level radiation test data. Previous work by Koontz, et al.1 utilized FLUKA, a Monte Carlo nuclear reaction and transport code, to calculate SEE and single event upset (SEU) rates. This code was then validated against in-flight data for a variety of spacecraft and space flight environments. However, FLUKA has a long run-time (on the order of days). CREME962, an easy to use deterministic code offering short run times, was also compared with FLUKA predictions and in-flight data. CREME96, though fast and easy to use, has not been updated in several years and underestimates secondary particle shower effects in spacecraft structural shielding mass. Thus, this paper will investigate the use of HZETRN 20103, a fast and easy to use deterministic transport code, similar to CREME96, that was developed at NASA Langley Research Center primarily for flight crew ionizing radiation dose assessments. HZETRN 2010 includes updates to address secondary particle shower effects more accurately, and might be used as another tool to verify spacecraft avionics system reliability in space flight SEE environments.

Discrete Event-based Performance Prediction for Temperature Accelerated Dynamics

NASA Astrophysics Data System (ADS)

Junghans, Christoph; Mniszewski, Susan; Voter, Arthur; Perez, Danny; Eidenbenz, Stephan

2014-03-01

We present an example of a new class of tools that we call application simulators, parameterized fast-running proxies of large-scale scientific applications using parallel discrete event simulation (PDES). We demonstrate our approach with a TADSim application simulator that models the Temperature Accelerated Dynamics (TAD) method, which is an algorithmically complex member of the Accelerated Molecular Dynamics (AMD) family. The essence of the TAD application is captured without the computational expense and resource usage of the full code. We use TADSim to quickly characterize the runtime performance and algorithmic behavior for the otherwise long-running simulation code. We further extend TADSim to model algorithm extensions to standard TAD, such as speculative spawning of the compute-bound stages of the algorithm, and predict performance improvements without having to implement such a method. Focused parameter scans have allowed us to study algorithm parameter choices over far more scenarios than would be possible with the actual simulation. This has led to interesting performance-related insights into the TAD algorithm behavior and suggested extensions to the TAD method.

A Monte Carlo model system for core analysis and epithermal neutron beam design at the Washington State University Radiation Center

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

Burns, T.D. Jr.

1996-05-01

The Monte Carlo Model System (MCMS) for the Washington State University (WSU) Radiation Center provides a means through which core criticality and power distributions can be calculated, as well as providing a method for neutron and photon transport necessary for BNCT epithermal neutron beam design. The computational code used in this Model System is MCNP4A. The geometric capability of this Monte Carlo code allows the WSU system to be modeled very accurately. A working knowledge of the MCNP4A neutron transport code increases the flexibility of the Model System and is recommended, however, the eigenvalue/power density problems can be run withmore » little direct knowledge of MCNP4A. Neutron and photon particle transport require more experience with the MCNP4A code. The Model System consists of two coupled subsystems; the Core Analysis and Source Plane Generator Model (CASP), and the BeamPort Shell Particle Transport Model (BSPT). The CASP Model incorporates the S({alpha}, {beta}) thermal treatment, and is run as a criticality problem yielding, the system eigenvalue (k{sub eff}), the core power distribution, and an implicit surface source for subsequent particle transport in the BSPT Model. The BSPT Model uses the source plane generated by a CASP run to transport particles through the thermal column beamport. The user can create filter arrangements in the beamport and then calculate characteristics necessary for assessing the BNCT potential of the given filter want. Examples of the characteristics to be calculated are: neutron fluxes, neutron currents, fast neutron KERMAs and gamma KERMAs. The MCMS is a useful tool for the WSU system. Those unfamiliar with the MCNP4A code can use the MCMS transparently for core analysis, while more experienced users will find the particle transport capabilities very powerful for BNCT filter design.« less

Fast Running Urban Dispersion Model for Radiological Dispersal Device (RDD) Releases: Model Description and Validation

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

Gowardhan, Akshay; Neuscamman, Stephanie; Donetti, John

Aeolus is an efficient three-dimensional computational fluid dynamics code based on finite volume method developed for predicting transport and dispersion of contaminants in a complex urban area. It solves the time dependent incompressible Navier-Stokes equation on a regular Cartesian staggered grid using a fractional step method. It also solves a scalar transport equation for temperature and using the Boussinesq approximation. The model also includes a Lagrangian dispersion model for predicting the transport and dispersion of atmospheric contaminants. The model can be run in an efficient Reynolds Average Navier-Stokes (RANS) mode with a run time of several minutes, or a moremore » detailed Large Eddy Simulation (LES) mode with run time of hours for a typical simulation. This report describes the model components, including details on the physics models used in the code, as well as several model validation efforts. Aeolus wind and dispersion predictions are compared to field data from the Joint Urban Field Trials 2003 conducted in Oklahoma City (Allwine et al 2004) including both continuous and instantaneous releases. Newly implemented Aeolus capabilities include a decay chain model and an explosive Radiological Dispersal Device (RDD) source term; these capabilities are described. Aeolus predictions using the buoyant explosive RDD source are validated against two experimental data sets: the Green Field explosive cloud rise experiments conducted in Israel (Sharon et al 2012) and the Full-Scale RDD Field Trials conducted in Canada (Green et al 2016).« less

Plasma Physics Calculations on a Parallel Macintosh Cluster

NASA Astrophysics Data System (ADS)

Decyk, Viktor; Dauger, Dean; Kokelaar, Pieter

2000-03-01

We have constructed a parallel cluster consisting of 16 Apple Macintosh G3 computers running the MacOS, and achieved very good performance on numerically intensive, parallel plasma particle-in-cell simulations. A subset of the MPI message-passing library was implemented in Fortran77 and C. This library enabled us to port code, without modification, from other parallel processors to the Macintosh cluster. For large problems where message packets are large and relatively few in number, performance of 50-150 MFlops/node is possible, depending on the problem. This is fast enough that 3D calculations can be routinely done. Unlike Unix-based clusters, no special expertise in operating systems is required to build and run the cluster. Full details are available on our web site: http://exodus.physics.ucla.edu/appleseed/.

Plasma Physics Calculations on a Parallel Macintosh Cluster

NASA Astrophysics Data System (ADS)

Decyk, Viktor K.; Dauger, Dean E.; Kokelaar, Pieter R.

We have constructed a parallel cluster consisting of 16 Apple Macintosh G3 computers running the MacOS, and achieved very good performance on numerically intensive, parallel plasma particle-in-cell simulations. A subset of the MPI message-passing library was implemented in Fortran77 and C. This library enabled us to port code, without modification, from other parallel processors to the Macintosh cluster. For large problems where message packets are large and relatively few in number, performance of 50-150 Mflops/node is possible, depending on the problem. This is fast enough that 3D calculations can be routinely done. Unlike Unix-based clusters, no special expertise in operating systems is required to build and run the cluster. Full details are available on our web site: http://exodus.physics.ucla.edu/appleseed/.

Coupled Kinetic-MHD Simulations of Divertor Heat Load with ELM Perturbations

NASA Astrophysics Data System (ADS)

Cummings, Julian; Chang, C. S.; Park, Gunyoung; Sugiyama, Linda; Pankin, Alexei; Klasky, Scott; Podhorszki, Norbert; Docan, Ciprian; Parashar, Manish

2010-11-01

The effect of Type-I ELM activity on divertor plate heat load is a key component of the DOE OFES Joint Research Target milestones for this year. In this talk, we present simulations of kinetic edge physics, ELM activity, and the associated divertor heat loads in which we couple the discrete guiding-center neoclassical transport code XGC0 with the nonlinear extended MHD code M3D using the End-to-end Framework for Fusion Integrated Simulations, or EFFIS. In these coupled simulations, the kinetic code and the MHD code run concurrently on the same massively parallel platform and periodic data exchanges are performed using a memory-to-memory coupling technology provided by EFFIS. The M3D code models the fast ELM event and sends frequent updates of the magnetic field perturbations and electrostatic potential to XGC0, which in turn tracks particle dynamics under the influence of these perturbations and collects divertor particle and energy flux statistics. We describe here how EFFIS technologies facilitate these coupled simulations and discuss results for DIII-D, NSTX and Alcator C-Mod tokamak discharges.

Investigation of HZETRN 2010 as a Tool for Single Event Effect Qualification of Avionics Systems - Part II

NASA Technical Reports Server (NTRS)

Rojdev, Kristina; Koontz, Steve; Reddell, Brandon; Atwell, William; Boeder, Paul

2015-01-01

An accurate prediction of spacecraft avionics single event effect (SEE) radiation susceptibility is key to ensuring a safe and reliable vehicle. This is particularly important for long-duration deep space missions for human exploration where there is little or no chance for a quick emergency return to Earth. Monte Carlo nuclear reaction and transport codes such as FLUKA can be used to generate very accurate models of the expected in-flight radiation environment for SEE analyses. A major downside to using a Monte Carlo-based code is that the run times can be very long (on the order of days). A more popular choice for SEE calculations is the CREME96 deterministic code, which offers significantly shorter run times (on the order of seconds). However, CREME96, though fast and easy to use, has not been updated in several years and underestimates secondary particle shower effects in spacecraft structural shielding mass. Another modeling option to consider is the deterministic code HZETRN 20104, which includes updates to address secondary particle shower effects more accurately. This paper builds on previous work by Rojdev, et al. to compare the use of HZETRN 2010 against CREME96 as a tool to verify spacecraft avionics system reliability in a space flight SEE environment. This paper will discuss modifications made to HZETRN 2010 to improve its performance for calculating SEE rates and compare results with both in-flight SEE rates and other calculation methods.

Minimizing embedding impact in steganography using trellis-coded quantization

NASA Astrophysics Data System (ADS)

Filler, Tomáš; Judas, Jan; Fridrich, Jessica

2010-01-01

In this paper, we propose a practical approach to minimizing embedding impact in steganography based on syndrome coding and trellis-coded quantization and contrast its performance with bounds derived from appropriate rate-distortion bounds. We assume that each cover element can be assigned a positive scalar expressing the impact of making an embedding change at that element (single-letter distortion). The problem is to embed a given payload with minimal possible average embedding impact. This task, which can be viewed as a generalization of matrix embedding or writing on wet paper, has been approached using heuristic and suboptimal tools in the past. Here, we propose a fast and very versatile solution to this problem that can theoretically achieve performance arbitrarily close to the bound. It is based on syndrome coding using linear convolutional codes with the optimal binary quantizer implemented using the Viterbi algorithm run in the dual domain. The complexity and memory requirements of the embedding algorithm are linear w.r.t. the number of cover elements. For practitioners, we include detailed algorithms for finding good codes and their implementation. Finally, we report extensive experimental results for a large set of relative payloads and for different distortion profiles, including the wet paper channel.

Efficient full wave code for the coupling of large multirow multijunction LH grills

NASA Astrophysics Data System (ADS)

Preinhaelter, Josef; Hillairet, Julien; Milanesio, Daniele; Maggiora, Riccardo; Urban, Jakub; Vahala, Linda; Vahala, George

2017-11-01

The full wave code OLGA, for determining the coupling of a single row lower hybrid launcher (waveguide grills) to the plasma, is extended to handle multirow multijunction active passive structures (like the C3 and C4 launchers on TORE SUPRA) by implementing the scattering matrix formalism. The extended code is still computationally fast because of the use of (i) 2D splines of the plasma surface admittance in the accessibility region of the k-space, (ii) high order Gaussian quadrature rules for the integration of the coupling elements and (iii) utilizing the symmetries of the coupling elements in the multiperiodic structures. The extended OLGA code is benchmarked against the ALOHA-1D, ALOHA-2D and TOPLHA codes for the coupling of the C3 and C4 TORE SUPRA launchers for several plasma configurations derived from reflectometry and interferometery. Unlike nearly all codes (except the ALOHA-1D code), OLGA does not require large computational resources and can be used for everyday usage in planning experimental runs. In particular, it is shown that the OLGA code correctly handles the coupling of the C3 and C4 launchers over a very wide range of plasma densities in front of the grill.

ACON: a multipurpose production controller for plasma physics codes

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

Snell, C.

1983-01-01

ACON is a BCON controller designed to run large production codes on the CTSS Cray-1 or the LTSS 7600 computers. ACON can also be operated interactively, with input from the user's terminal. The controller can run one code or a sequence of up to ten codes during the same job. Options are available to get and save Mass storage files, to perform Historian file updating operations, to compile and load source files, and to send out print and film files. Special features include ability to retry after Mass failures, backup options for saving files, startup messages for the various codes,more » and ability to reserve specified amounts of computer time after successive code runs. ACON's flexibility and power make it useful for running a number of different production codes.« less

Classification Techniques for Digital Map Compression

DTIC Science & Technology

1989-03-01

classification improved the performance of the K-means classification algorithm resulting in a compression of 8.06:1 with Lempel - Ziv coding. Run-length coding... compression performance are run-length coding [2], [8] and Lempel - Ziv coding 110], [11]. These techniques are chosen because they are most efficient when...investigated. After the classification, some standard file compression methods, such as Lempel - Ziv and run-length encoding were applied to the

Mechanistic prediction of fission-gas behavior during in-cell transient heating tests on LWR fuel using the GRASS-SST and FASTGRASS computer codes

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

Rest, J; Gehl, S M

1979-01-01

GRASS-SST and FASTGRASS are mechanistic computer codes for predicting fission-gas behavior in UO/sub 2/-base fuels during steady-state and transient conditions. FASTGRASS was developed in order to satisfy the need for a fast-running alternative to GRASS-SST. Althrough based on GRASS-SST, FASTGRASS is approximately an order of magnitude quicker in execution. The GRASS-SST transient analysis has evolved through comparisons of code predictions with the fission-gas release and physical phenomena that occur during reactor operation and transient direct-electrical-heating (DEH) testing of irradiated light-water reactor fuel. The FASTGRASS calculational procedure is described in this paper, along with models of key physical processes included inmore » both FASTGRASS and GRASS-SST. Predictions of fission-gas release obtained from GRASS-SST and FASTGRASS analyses are compared with experimental observations from a series of DEH tests. The major conclusions is that the computer codes should include an improved model for the evolution of the grain-edge porosity.« less

CFD analyses for advanced pump design

NASA Technical Reports Server (NTRS)

Dejong, F. J.; Choi, S.-K.; Govindan, T. R.

1994-01-01

As one of the activities of the NASA/MSFC Pump Stage Technology Team, the present effort was focused on using CFD in the design and analysis of high performance rocket engine pumps. Under this effort, a three-dimensional Navier-Stokes code was used for various inducer and impeller flow field calculations. An existing algebraic grid generation procedure was-extended to allow for nonzero blade thickness, splitter blades, and hub/shroud cavities upstream or downstream of the (main) blades. This resulted in a fast, robust inducer/impeller geometry/grid generation package. Problems associated with running a compressible flow code to simulate an incompressible flow were resolved; related aspects of the numerical algorithm (viz., the matrix preconditioning, the artificial dissipation, and the treatment of low Mach number flows) were addressed. As shown by the calculations performed under the present effort, the resulting code, in conjunction with the grid generation package, is an effective tool for the rapid solution of three-dimensional viscous inducer and impeller flows.

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.

EnergyPlus Run Time Analysis

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

Hong, Tianzhen; Buhl, Fred; Haves, Philip

2008-09-20

EnergyPlus is a new generation building performance simulation program offering many new modeling capabilities and more accurate performance calculations integrating building components in sub-hourly time steps. However, EnergyPlus runs much slower than the current generation simulation programs. This has become a major barrier to its widespread adoption by the industry. This paper analyzed EnergyPlus run time from comprehensive perspectives to identify key issues and challenges of speeding up EnergyPlus: studying the historical trends of EnergyPlus run time based on the advancement of computers and code improvements to EnergyPlus, comparing EnergyPlus with DOE-2 to understand and quantify the run time differences,more » identifying key simulation settings and model features that have significant impacts on run time, and performing code profiling to identify which EnergyPlus subroutines consume the most amount of run time. This paper provides recommendations to improve EnergyPlus run time from the modeler?s perspective and adequate computing platforms. Suggestions of software code and architecture changes to improve EnergyPlus run time based on the code profiling results are also discussed.« less

Slow Orbit Feedback at the ALS Using Matlab

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

Portmann, G.

1999-03-25

The third generation Advanced Light Source (ALS) produces extremely bright and finely focused photon beams using undulatory, wigglers, and bend magnets. In order to position the photon beams accurately, a slow global orbit feedback system has been developed. The dominant causes of orbit motion at the ALS are temperature variation and insertion device motion. This type of motion can be removed using slow global orbit feedback with a data rate of a few Hertz. The remaining orbit motion in the ALS is only 1-3 micron rms. Slow orbit feedback does not require high computational throughput. At the ALS, the globalmore » orbit feedback algorithm, based on the singular valued decomposition method, is coded in MATLAB and runs on a control room workstation. Using the MATLAB environment to develop, test, and run the storage ring control algorithms has proven to be a fast and efficient way to operate the ALS.« less

A Novel Technique for Running the NASA Legacy Code LAPIN Synchronously With Simulations Developed Using Simulink

NASA Technical Reports Server (NTRS)

Vrnak, Daniel R.; Stueber, Thomas J.; Le, Dzu K.

2012-01-01

This report presents a method for running a dynamic legacy inlet simulation in concert with another dynamic simulation that uses a graphical interface. The legacy code, NASA's LArge Perturbation INlet (LAPIN) model, was coded using the FORTRAN 77 (The Portland Group, Lake Oswego, OR) programming language to run in a command shell similar to other applications that used the Microsoft Disk Operating System (MS-DOS) (Microsoft Corporation, Redmond, WA). Simulink (MathWorks, Natick, MA) is a dynamic simulation that runs on a modern graphical operating system. The product of this work has both simulations, LAPIN and Simulink, running synchronously on the same computer with periodic data exchanges. Implementing the method described in this paper avoided extensive changes to the legacy code and preserved its basic operating procedure. This paper presents a novel method that promotes inter-task data communication between the synchronously running processes.

Effects of Ramadan intermittent fasting on middle-distance running performance in well-trained runners.

PubMed

Brisswalter, Jeanick; Bouhlel, Ezzedine; Falola, Jean Marie; Abbiss, Christopher R; Vallier, Jean Marc; Hausswirth, Christophe; Hauswirth, Christophe

2011-09-01

To assess whether Ramadan intermittent fasting (RIF) affects 5000-m running performance and physiological parameters classically associated with middle-distance performance. Two experimental groups (Ramadan fasting, n = 9, vs control, n = 9) participated in 2 experimental sessions, one before RIF and the other at the last week of fasting. For each session, subjects completed 4 tests in the same order: a maximal running test, a maximal voluntary contraction (MVC) of knee extensor, 2 rectangular submaximal exercises on treadmill for 6 minutes at an intensity corresponding to the first ventilatory threshold (VT1), and a running performance test (5000 m). Eighteen, well-trained, middle-distance runners. Maximal oxygen consumption, MVC, running performance, running efficiency, submaximal VO(2) kinetics parameters (VO(2), VO(2)b, time constant τ, and amplitude A1) and anthropometric parameters were recorded or calculated. At the end of Ramadan fasting, a decrease in MVC was observed (-3.2%; P < 0.00001; η, 0.80), associated with an increase in the time constant of oxygen kinetics (+51%; P < 0.00007; η, 0.72) and a decrease in performance (-5%; P < 0.0007; η, 0.51). No effect was observed on running efficiency or maximal aerobic power. These results suggest that Ramadan changes in muscular performance and oxygen kinetics could affect performance during middle-distance events and need to be considered to choose training protocols during RIF.

Fingerprinting Communication and Computation on HPC Machines

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

Peisert, Sean

2010-06-02

How do we identify what is actually running on high-performance computing systems? Names of binaries, dynamic libraries loaded, or other elements in a submission to a batch queue can give clues, but binary names can be changed, and libraries provide limited insight and resolution on the code being run. In this paper, we present a method for"fingerprinting" code running on HPC machines using elements of communication and computation. We then discuss how that fingerprint can be used to determine if the code is consistent with certain other types of codes, what a user usually runs, or what the user requestedmore » an allocation to do. In some cases, our techniques enable us to fingerprint HPC codes using runtime MPI data with a high degree of accuracy.« less

A Wideband Fast Multipole Method for the two-dimensional complex Helmholtz equation

NASA Astrophysics Data System (ADS)

Cho, Min Hyung; Cai, Wei

2010-12-01

A Wideband Fast Multipole Method (FMM) for the 2D Helmholtz equation is presented. It can evaluate the interactions between N particles governed by the fundamental solution of 2D complex Helmholtz equation in a fast manner for a wide range of complex wave number k, which was not easy with the original FMM due to the instability of the diagonalized conversion operator. This paper includes the description of theoretical backgrounds, the FMM algorithm, software structures, and some test runs. Program summaryProgram title: 2D-WFMM Catalogue identifier: AEHI_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHI_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 4636 No. of bytes in distributed program, including test data, etc.: 82 582 Distribution format: tar.gz Programming language: C Computer: Any Operating system: Any operating system with gcc version 4.2 or newer Has the code been vectorized or parallelized?: Multi-core processors with shared memory RAM: Depending on the number of particles N and the wave number k Classification: 4.8, 4.12 External routines: OpenMP ( http://openmp.org/wp/) Nature of problem: Evaluate interaction between N particles governed by the fundamental solution of 2D Helmholtz equation with complex k. Solution method: Multilevel Fast Multipole Algorithm in a hierarchical quad-tree structure with cutoff level which combines low frequency method and high frequency method. Running time: Depending on the number of particles N, wave number k, and number of cores in CPU. CPU time increases as N log N.

An Accurate and Efficient Algorithm for Detection of Radio Bursts with an Unknown Dispersion Measure, for Single-dish Telescopes and Interferometers

NASA Astrophysics Data System (ADS)

Zackay, Barak; Ofek, Eran O.

2017-01-01

Astronomical radio signals are subjected to phase dispersion while traveling through the interstellar medium. To optimally detect a short-duration signal within a frequency band, we have to precisely compensate for the unknown pulse dispersion, which is a computationally demanding task. We present the “fast dispersion measure transform” algorithm for optimal detection of such signals. Our algorithm has a low theoretical complexity of 2{N}f{N}t+{N}t{N}{{Δ }}{{log}}2({N}f), where Nf, Nt, and NΔ are the numbers of frequency bins, time bins, and dispersion measure bins, respectively. Unlike previously suggested fast algorithms, our algorithm conserves the sensitivity of brute-force dedispersion. Our tests indicate that this algorithm, running on a standard desktop computer and implemented in a high-level programming language, is already faster than the state-of-the-art dedispersion codes running on graphical processing units (GPUs). We also present a variant of the algorithm that can be efficiently implemented on GPUs. The latter algorithm’s computation and data-transport requirements are similar to those of a two-dimensional fast Fourier transform, indicating that incoherent dedispersion can now be considered a nonissue while planning future surveys. We further present a fast algorithm for sensitive detection of pulses shorter than the dispersive smearing limits of incoherent dedispersion. In typical cases, this algorithm is orders of magnitude faster than enumerating dispersion measures and coherently dedispersing by convolution. We analyze the computational complexity of pulsed signal searches by radio interferometers. We conclude that, using our suggested algorithms, maximally sensitive blind searches for dispersed pulses are feasible using existing facilities. We provide an implementation of these algorithms in Python and MATLAB.

Frog: The fast & realistic OpenGL event displayer

NASA Astrophysics Data System (ADS)

Quertenmont, Loïc

2010-04-01

FROG [1] [2] is a generic framework dedicated to visualisation of events in high energy physics experiment. It is suitable to any particular physics experiment or detector design. The code is light (< 3 MB) and fast (browsing time ~ 20 events per second for a large High Energy Physics experiment) and can run on various operating systems, as its object-oriented structure (C++) relies on the cross-platform OpenGL[3] and Glut [4] libraries. Moreover, Frog does not require installation of heavy third party libraries for the visualisation. This documents describes the features and principles of Frog version 1.106, its working scheme and numerous functionalities such as: 3D and 2D visualisation, graphical user interface, mouse interface, configuration files, production of pictures of various format, integration of personal objects, etc. Finally the application of FROG for physic experiment/environement, such as Gastof, CMS, ILD, Delphes will be presented for illustration.

Potential Application of a Graphical Processing Unit to Parallel Computations in the NUBEAM Code

NASA Astrophysics Data System (ADS)

Payne, J.; McCune, D.; Prater, R.

2010-11-01

NUBEAM is a comprehensive computational Monte Carlo based model for neutral beam injection (NBI) in tokamaks. NUBEAM computes NBI-relevant profiles in tokamak plasmas by tracking the deposition and the slowing of fast ions. At the core of NUBEAM are vector calculations used to track fast ions. These calculations have recently been parallelized to run on MPI clusters. However, cost and interlink bandwidth limit the ability to fully parallelize NUBEAM on an MPI cluster. Recent implementation of double precision capabilities for Graphical Processing Units (GPUs) presents a cost effective and high performance alternative or complement to MPI computation. Commercially available graphics cards can achieve up to 672 GFLOPS double precision and can handle hundreds of thousands of threads. The ability to execute at least one thread per particle simultaneously could significantly reduce the execution time and the statistical noise of NUBEAM. Progress on implementation on a GPU will be presented.

FAST - FREEDOM ASSEMBLY SEQUENCING TOOL PROTOTYPE

NASA Technical Reports Server (NTRS)

Borden, C. S.

1994-01-01

FAST is a project management tool designed to optimize the assembly sequence of Space Station Freedom. An appropriate assembly sequence coordinates engineering, design, utilization, transportation availability, and operations requirements. Since complex designs tend to change frequently, FAST assesses the system level effects of detailed changes and produces output metrics that identify preferred assembly sequences. FAST incorporates Space Shuttle integration, Space Station hardware, on-orbit operations, and programmatic drivers as either precedence relations or numerical data. Hardware sequencing information can either be input directly and evaluated via the "specified" mode of operation or evaluated from the input precedence relations in the "flexible" mode. In the specified mode, FAST takes as its input a list of the cargo elements assigned to each flight. The program determines positions for the cargo elements that maximize the center of gravity (c.g.) margin. These positions are restricted by the geometry of the cargo elements and the location of attachment fittings both in the orbiter and on the cargo elements. FAST calculates every permutation of cargo element location according to its height, trunnion fitting locations, and required intercargo element spacing. Each cargo element is tested in both its normal and reversed orientation (rotated 180 degrees). The best solution is that which maximizes the c.g. margin for each flight. In the flexible mode, FAST begins with the first flight and determines all feasible combinations of cargo elements according to mass, volume, EVA, and precedence relation constraints. The program generates an assembly sequence that meets mass, volume, position, EVA, and precedence constraints while minimizing the total number of Shuttle flights required. Issues associated with ground operations, spacecraft performance, logistics requirements and user requirements will be addressed in future versions of the model. FAST is written in C-Language and has been implemented on DEC VAX series computers running VMS. The program is distributed in executable form. The source code is also provided, but it cannot be compiled without the Tree Manipulation Based Routines (TMBR) package from the Jet Propulsion Laboratory, which is not currently available from COSMIC. The main memory requirement is based on the data used to drive the FAST program. All applications should easily run on an installation with 10Mb of main memory. FAST was developed in 1990 and is a copyrighted work with all copyright vested in NASA. DEC, VAX and VMS are trademarks of Digital Equipment Corporation.

The new Gemini Observatory archive: a fast and low cost observatory data archive running in the cloud

NASA Astrophysics Data System (ADS)

Hirst, Paul; Cardenes, Ricardo

2016-08-01

We have developed and deployed a new data archive for the Gemini Observatory. Focused on simplicity and ease of use, the archive provides a number of powerful and novel features including automatic association of calibration data with the science data, and the ability to bookmark searches. A simple but powerful API allows programmatic search and download of data. The archive is hosted on Amazon Web Services, which provides us excellent internet connectivity and significant cost savings in both operations and development over more traditional deployment options. The code is written in python, utilizing a PostgreSQL database and Apache web server.

State-Of High Brightness RF Photo-Injector Design

NASA Astrophysics Data System (ADS)

Ferrario, Massimo; Clendenin, Jym; Palmer, Dennis; Rosenzweig, James; Serafini, Luca

2000-04-01

The art of designing optimized high brightness electron RF Photo-Injectors has moved in the last decade from a cut and try procedure, guided by experimental experience and time consuming particle tracking simulations, up to a fast parameter space scanning, guided by recent analytical results and a fast running semi-analytical code, so to reach the optimum operating point which corresponds to maximum beam brightness. Scaling laws and the theory of invariant envelope provide to the designers excellent tools for a first parameters choice and the code HOMDYN, based on a multi-slice envelope description of the beam dynamics, is tailored to describe the space charge dominated dynamics of laminar beams in presence of time dependent space charge forces, giving rise to a very fast modeling capability for photo-injectors design. We report in this talk the results of a recent beam dynamics study, motivated by the need to redesign the LCLS photoinjector. During this work a new effective working point for a split RF photoinjector has been discovered by means of the previous mentioned approach. By a proper choice of rf gun and solenoid parameters, the emittance evolution shows a double minimum behavior in the drifting region. If the booster is located where the relative emittance maximum and the envelope waist occur, the second emittance minimum can be shifted at the booster exit and frozen at a very low level (0.3 mm-mrad for a 1 nC flat top bunch), to the extent that the invariant envelope matching conditions are satisfied.

Transport Simulations for Fast Ignition on NIF

NASA Astrophysics Data System (ADS)

Strozzi, D. J.; Tabak, M.; Grote, D. P.; Town, R. P. J.; Kemp, A. J.

2009-11-01

Calculations of the transport and deposition of a relativistic electron beam into fast-ignition fuel configurations are presented. The hybrid PIC code LSP is used, run in implicit mode and with fluid background particles. The electron beam distribution is chosen based on explicit PIC simulations of the short-pulse LPI. These generally display two hot-electron temperatures, one close to the ponderomotive scaling and one that is much lower. Fast-electron collisions utilize the formulae of J. R. Davies [S. Atzeni et al., Plasma Phys. Controlled Fusion 51 (2009)], and are done with a conservative, relativistic grid-based method similar to Lemons et al., J. Comput. Phys. 228 (2009). We include energy loss off both bound and free electrons in partially-ionized media (such as a gold cone), and have started to use realistic ionization and non-ideal EOS models. We have found the fractional energy coupling into the dense fuel is higher for CD than DT targets, due to the enhanced resistivity and resulting magnetic fields. The coupling enhancement due to magnetic fields and beam characteristics (such as angular spectrum) will be quantified.

PCEMCAN - Probabilistic Ceramic Matrix Composites Analyzer: User's Guide, Version 1.0

NASA Technical Reports Server (NTRS)

Shah, Ashwin R.; Mital, Subodh K.; Murthy, Pappu L. N.

1998-01-01

PCEMCAN (Probabalistic CEramic Matrix Composites ANalyzer) is an integrated computer code developed at NASA Lewis Research Center that simulates uncertainties associated with the constituent properties, manufacturing process, and geometric parameters of fiber reinforced ceramic matrix composites and quantifies their random thermomechanical behavior. The PCEMCAN code can perform the deterministic as well as probabilistic analyses to predict thermomechanical properties. This User's guide details the step-by-step procedure to create input file and update/modify the material properties database required to run PCEMCAN computer code. An overview of the geometric conventions, micromechanical unit cell, nonlinear constitutive relationship and probabilistic simulation methodology is also provided in the manual. Fast probability integration as well as Monte-Carlo simulation methods are available for the uncertainty simulation. Various options available in the code to simulate probabilistic material properties and quantify sensitivity of the primitive random variables have been described. The description of deterministic as well as probabilistic results have been described using demonstration problems. For detailed theoretical description of deterministic and probabilistic analyses, the user is referred to the companion documents "Computational Simulation of Continuous Fiber-Reinforced Ceramic Matrix Composite Behavior," NASA TP-3602, 1996 and "Probabilistic Micromechanics and Macromechanics for Ceramic Matrix Composites", NASA TM 4766, June 1997.

Parameterized code SHARM-3D for radiative transfer over inhomogeneous surfaces.

PubMed

Lyapustin, Alexei; Wang, Yujie

2005-12-10

The code SHARM-3D, developed for fast and accurate simulations of the monochromatic radiance at the top of the atmosphere over spatially variable surfaces with Lambertian or anisotropic reflectance, is described. The atmosphere is assumed to be laterally uniform across the image and to consist of two layers with aerosols contained in the bottom layer. The SHARM-3D code performs simultaneous calculations for all specified incidence-view geometries and multiple wavelengths in one run. The numerical efficiency of the current version of code is close to its potential limit and is achieved by means of two innovations. The first is the development of a comprehensive precomputed lookup table of the three-dimensional atmospheric optical transfer function for various atmospheric conditions. The second is the use of a linear kernel model of the land surface bidirectional reflectance factor (BRF) in our algorithm that has led to a fully parameterized solution in terms of the surface BRF parameters. The code is also able to model inland lakes and rivers. The water pixels are described with the Nakajima-Tanaka BRF model of wind-roughened water surface with a Lambertian offset, which is designed to model approximately the reflectance of suspended matter and of a shallow lake or river bottom.

Parameterized code SHARM-3D for radiative transfer over inhomogeneous surfaces

NASA Astrophysics Data System (ADS)

Lyapustin, Alexei; Wang, Yujie

2005-12-01

The code SHARM-3D, developed for fast and accurate simulations of the monochromatic radiance at the top of the atmosphere over spatially variable surfaces with Lambertian or anisotropic reflectance, is described. The atmosphere is assumed to be laterally uniform across the image and to consist of two layers with aerosols contained in the bottom layer. The SHARM-3D code performs simultaneous calculations for all specified incidence-view geometries and multiple wavelengths in one run. The numerical efficiency of the current version of code is close to its potential limit and is achieved by means of two innovations. The first is the development of a comprehensive precomputed lookup table of the three-dimensional atmospheric optical transfer function for various atmospheric conditions. The second is the use of a linear kernel model of the land surface bidirectional reflectance factor (BRF) in our algorithm that has led to a fully parameterized solution in terms of the surface BRF parameters. The code is also able to model inland lakes and rivers. The water pixels are described with the Nakajima-Tanaka BRF model of wind-roughened water surface with a Lambertian offset, which is designed to model approximately the reflectance of suspended matter and of a shallow lake or river bottom.

Fast and Adaptive Lossless Onboard Hyperspectral Data Compression System

NASA Technical Reports Server (NTRS)

Aranki, Nazeeh I.; Keymeulen, Didier; Kimesh, Matthew A.

2012-01-01

Modern hyperspectral imaging systems are able to acquire far more data than can be downlinked from a spacecraft. Onboard data compression helps to alleviate this problem, but requires a system capable of power efficiency and high throughput. Software solutions have limited throughput performance and are power-hungry. Dedicated hardware solutions can provide both high throughput and power efficiency, while taking the load off of the main processor. Thus a hardware compression system was developed. The implementation uses a field-programmable gate array (FPGA). The implementation is based on the fast lossless (FL) compression algorithm reported in Fast Lossless Compression of Multispectral-Image Data (NPO-42517), NASA Tech Briefs, Vol. 30, No. 8 (August 2006), page 26, which achieves excellent compression performance and has low complexity. This algorithm performs predictive compression using an adaptive filtering method, and uses adaptive Golomb coding. The implementation also packetizes the coded data. The FL algorithm is well suited for implementation in hardware. In the FPGA implementation, one sample is compressed every clock cycle, which makes for a fast and practical realtime solution for space applications. Benefits of this implementation are: 1) The underlying algorithm achieves a combination of low complexity and compression effectiveness that exceeds that of techniques currently in use. 2) The algorithm requires no training data or other specific information about the nature of the spectral bands for a fixed instrument dynamic range. 3) Hardware acceleration provides a throughput improvement of 10 to 100 times vs. the software implementation. A prototype of the compressor is available in software, but it runs at a speed that does not meet spacecraft requirements. The hardware implementation targets the Xilinx Virtex IV FPGAs, and makes the use of this compressor practical for Earth satellites as well as beyond-Earth missions with hyperspectral instruments.

Skills Associated with Line Breaks in Elite Rugby Union

PubMed Central

den Hollander, Steve; Brown, James; Lambert, Michael; Treu, Paul; Hendricks, Sharief

2016-01-01

The ability of the attacking team to break through the defensive line is a key indicator of success as it creates opportunities to score tries. The aim of this study was to analyse line breaks and identify the associated skills and playing characteristics. The 2013 Super Rugby season (125 games) was analysed, in which 362 line breaks were identified and coded using variables that assessed team patterns and non-contact attacking skills in the phases preceding the line break. There was an average of 3 line breaks per game, with 39% of line breaks resulting in a try. Line breaks occurred when the ball-carrier was running fast [61%, x2(4) = 25.784, p = 0.000, Cramer’s v = 0.1922, weak]. At a moderate distance, short lateral passes (19%) and skip passes (15%) attributed to the highest percentage of line breaks [x2(26) = 50.899, p = 0.036, Cramer’s v = 0.2484, moderate]. Faster defensive line speeds resulted in more line breaks [x2(12) = 61.703, p < 0.001, Cramer’s v = 0.3026, moderate]. Line breaks are associated with overall team success and try scoring opportunities. Awareness of the defenders line speed and depth, fast running speed when receiving the ball and quick passing between attackers to the outside backs creates line break opportunities. During training, coaches should emphasise the movement speed of the ball between attackers and manipulate the speed and distance of the defenders. Key points Line breaks are associated with overall team success and try scoring opportunities. Awareness of the defenders line speed and depth, fast running speed when receiving the ball and quick passing between attackers to the outside backs creates line break opportunities During training, coaches should emphasise the movement speed of the ball between attackers and manipulate the speed and distance of the defenders. PMID:27803629

CASL VMA FY16 Milestone Report (L3:VMA.VUQ.P13.07) Westinghouse Mixing with COBRA-TF

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

Gordon, Natalie

2016-09-30

COBRA-TF (CTF) is a low-resolution code currently maintained as CASL's subchannel analysis tool. CTF operates as a two-phase, compressible code over a mesh comprised of subchannels and axial discretized nodes. In part because CTF is a low-resolution code, simulation run time is not computationally expensive, only on the order of minutes. Hi-resolution codes such as STAR-CCM+ can be used to train lower-fidelity codes such as CTF. Unlike STAR-CCM+, CTF has no turbulence model, only a two-phase turbulent mixing coefficient, β. β can be set to a constant value or calculated in terms of Reynolds number using an empirical correlation. Resultsmore » from STAR-CCM+ can be used to inform the appropriate value of β. Once β is calibrated, CTF runs can be an inexpensive alternative to costly STAR-CCM+ runs for scoping analyses. Based on the results of CTF runs, STAR-CCM+ can be run for specific parameters of interest. CASL areas of application are CIPS for single phase analysis and DNB-CTF for two-phase analysis.« less

Current and planned numerical development for improving computing performance for long duration and/or low pressure transients

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

Faydide, B.

1997-07-01

This paper presents the current and planned numerical development for improving computing performance in case of Cathare applications needing real time, like simulator applications. Cathare is a thermalhydraulic code developed by CEA (DRN), IPSN, EDF and FRAMATOME for PWR safety analysis. First, the general characteristics of the code are presented, dealing with physical models, numerical topics, and validation strategy. Then, the current and planned applications of Cathare in the field of simulators are discussed. Some of these applications were made in the past, using a simplified and fast-running version of Cathare (Cathare-Simu); the status of the numerical improvements obtained withmore » Cathare-Simu is presented. The planned developments concern mainly the Simulator Cathare Release (SCAR) project which deals with the use of the most recent version of Cathare inside simulators. In this frame, the numerical developments are related with the speed up of the calculation process, using parallel processing and improvement of code reliability on a large set of NPP transients.« less

The NEST Dry-Run Mode: Efficient Dynamic Analysis of Neuronal Network Simulation Code.

PubMed

Kunkel, Susanne; Schenck, Wolfram

2017-01-01

NEST is a simulator for spiking neuronal networks that commits to a general purpose approach: It allows for high flexibility in the design of network models, and its applications range from small-scale simulations on laptops to brain-scale simulations on supercomputers. Hence, developers need to test their code for various use cases and ensure that changes to code do not impair scalability. However, running a full set of benchmarks on a supercomputer takes up precious compute-time resources and can entail long queuing times. Here, we present the NEST dry-run mode, which enables comprehensive dynamic code analysis without requiring access to high-performance computing facilities. A dry-run simulation is carried out by a single process, which performs all simulation steps except communication as if it was part of a parallel environment with many processes. We show that measurements of memory usage and runtime of neuronal network simulations closely match the corresponding dry-run data. Furthermore, we demonstrate the successful application of the dry-run mode in the areas of profiling and performance modeling.

The NEST Dry-Run Mode: Efficient Dynamic Analysis of Neuronal Network Simulation Code

PubMed Central

Kunkel, Susanne; Schenck, Wolfram

2017-01-01

NEST is a simulator for spiking neuronal networks that commits to a general purpose approach: It allows for high flexibility in the design of network models, and its applications range from small-scale simulations on laptops to brain-scale simulations on supercomputers. Hence, developers need to test their code for various use cases and ensure that changes to code do not impair scalability. However, running a full set of benchmarks on a supercomputer takes up precious compute-time resources and can entail long queuing times. Here, we present the NEST dry-run mode, which enables comprehensive dynamic code analysis without requiring access to high-performance computing facilities. A dry-run simulation is carried out by a single process, which performs all simulation steps except communication as if it was part of a parallel environment with many processes. We show that measurements of memory usage and runtime of neuronal network simulations closely match the corresponding dry-run data. Furthermore, we demonstrate the successful application of the dry-run mode in the areas of profiling and performance modeling. PMID:28701946

Fast Acceleration of 2D Wave Propagation Simulations Using Modern Computational Accelerators

PubMed Central

Wang, Wei; Xu, Lifan; Cavazos, John; Huang, Howie H.; Kay, Matthew

2014-01-01

Recent developments in modern computational accelerators like Graphics Processing Units (GPUs) and coprocessors provide great opportunities for making scientific applications run faster than ever before. However, efficient parallelization of scientific code using new programming tools like CUDA requires a high level of expertise that is not available to many scientists. This, plus the fact that parallelized code is usually not portable to different architectures, creates major challenges for exploiting the full capabilities of modern computational accelerators. In this work, we sought to overcome these challenges by studying how to achieve both automated parallelization using OpenACC and enhanced portability using OpenCL. We applied our parallelization schemes using GPUs as well as Intel Many Integrated Core (MIC) coprocessor to reduce the run time of wave propagation simulations. We used a well-established 2D cardiac action potential model as a specific case-study. To the best of our knowledge, we are the first to study auto-parallelization of 2D cardiac wave propagation simulations using OpenACC. Our results identify several approaches that provide substantial speedups. The OpenACC-generated GPU code achieved more than speedup above the sequential implementation and required the addition of only a few OpenACC pragmas to the code. An OpenCL implementation provided speedups on GPUs of at least faster than the sequential implementation and faster than a parallelized OpenMP implementation. An implementation of OpenMP on Intel MIC coprocessor provided speedups of with only a few code changes to the sequential implementation. We highlight that OpenACC provides an automatic, efficient, and portable approach to achieve parallelization of 2D cardiac wave simulations on GPUs. Our approach of using OpenACC, OpenCL, and OpenMP to parallelize this particular model on modern computational accelerators should be applicable to other computational models of wave propagation in multi-dimensional media. PMID:24497950

Ground reaction forces in shallow water running are affected by immersion level, running speed and gender.

PubMed

Haupenthal, Alessandro; Fontana, Heiliane de Brito; Ruschel, Caroline; dos Santos, Daniela Pacheco; Roesler, Helio

2013-07-01

To analyze the effect of depth of immersion, running speed and gender on ground reaction forces during water running. Controlled laboratory study. Twenty adults (ten male and ten female) participated by running at two levels of immersion (hip and chest) and two speed conditions (slow and fast). Data were collected using an underwater force platform. The following variables were analyzed: vertical force peak (Fy), loading rate (LR) and anterior force peak (Fx anterior). Three-factor mixed ANOVA was used to analyze data. Significant effects of immersion level, speed and gender on Fy were observed, without interaction between factors. Fy was greater when females ran fast at the hip level. There was a significant increase in LR with a reduction in the level of immersion regardless of the speed and gender. No effect of speed or gender on LR was observed. Regarding Fx anterior, significant interaction between speed and immersion level was found: in the slow condition, participants presented greater values at chest immersion, whereas, during the fast running condition, greater values were observed at hip level. The effect of gender was only significant during fast water running, with Fx anterior being greater in the men group. Increasing speed raised Fx anterior significantly irrespective of the level of immersion and gender. The magnitude of ground reaction forces during shallow water running are affected by immersion level, running speed and gender and, for this reason, these factors should be taken into account during exercise prescription. Copyright © 2012 Sports Medicine Australia. Published by Elsevier Ltd. All rights reserved.

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.

TADSim: Discrete Event-based Performance Prediction for Temperature Accelerated Dynamics

DOE PAGES

Mniszewski, Susan M.; Junghans, Christoph; Voter, Arthur F.; ...

2015-04-16

Next-generation high-performance computing will require more scalable and flexible performance prediction tools to evaluate software--hardware co-design choices relevant to scientific applications and hardware architectures. Here, we present a new class of tools called application simulators—parameterized fast-running proxies of large-scale scientific applications using parallel discrete event simulation. Parameterized choices for the algorithmic method and hardware options provide a rich space for design exploration and allow us to quickly find well-performing software--hardware combinations. We demonstrate our approach with a TADSim simulator that models the temperature-accelerated dynamics (TAD) method, an algorithmically complex and parameter-rich member of the accelerated molecular dynamics (AMD) family ofmore » molecular dynamics methods. The essence of the TAD application is captured without the computational expense and resource usage of the full code. We accomplish this by identifying the time-intensive elements, quantifying algorithm steps in terms of those elements, abstracting them out, and replacing them by the passage of time. We use TADSim to quickly characterize the runtime performance and algorithmic behavior for the otherwise long-running simulation code. We extend TADSim to model algorithm extensions, such as speculative spawning of the compute-bound stages, and predict performance improvements without having to implement such a method. Validation against the actual TAD code shows close agreement for the evolution of an example physical system, a silver surface. Finally, focused parameter scans have allowed us to study algorithm parameter choices over far more scenarios than would be possible with the actual simulation. This has led to interesting performance-related insights and suggested extensions.« less

Time-Dependent Simulations of Fast-Wave Heated High-Non-Inductive-Fraction H-Mode Plasmas in the National Spherical Torus Experiment Upgrade

NASA Astrophysics Data System (ADS)

Taylor, Gary; Bertelli, Nicola; Gerhardt, Stefan P.; Hosea, Joel C.; Mueller, Dennis; Perkins, Rory J.; Poli, Francesca M.; Wilson, James R.; Raman, Roger

2017-10-01

30 MHz fast-wave heating may be an effective tool for non-inductively ramping low-current plasmas to a level suitable for initiating up to 12 MW of neutral beam injection on the National Spherical Tokamak Experiment Upgrade (NSTX-U). Previously on NSTX 30 MHz fast wave heating was shown to efficiently and rapidly heat electrons; at the NSTX maximum axial toroidal magnetic field (BT(0)) of 0.55 T, 1.4 MW of 30 MHz heating increased the central electron temperature from 0.2 to 2 keV in 30 ms and generated an H-mode plasma with a non-inductive fraction (fNI) ˜ 0.7 at a plasma current (Ip) of 300 kA. NSTX-U will operate at BT(0) up to 1 T, with up to 4 MW of 30 MHz power (Prf). Predictive TRANSP free boundary transport simulations, using the TORIC full wave spectral code to calculate the fast-wave heating and current drive, have been run for NSTX-U Ip = 300 kA H-mode plasmas. Favorable scaling of fNI with 30 MHz heating power is predicted, with fNI ≥ 1 for Prf ≥ 2 MW.

Nuclear shell model code CRUNCHER

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

Resler, D.A.; Grimes, S.M.

1988-05-01

A new nuclear shell model code CRUNCHER, patterned after the code VLADIMIR, has been developed. While CRUNCHER and VLADIMIR employ the techniques of an uncoupled basis and the Lanczos process, improvements in the new code allow it to handle much larger problems than the previous code and to perform them more efficiently. Tests involving a moderately sized calculation indicate that CRUNCHER running on a SUN 3/260 workstation requires approximately one-half the central processing unit (CPU) time required by VLADIMIR running on a CRAY-1 supercomputer.

Reducing EnergyPlus Run Time For Code Compliance Tools

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

Athalye, Rahul A.; Gowri, Krishnan; Schultz, Robert W.

2014-09-12

Integration of the EnergyPlus ™ simulation engine into performance-based code compliance software raises a concern about simulation run time, which impacts timely feedback of compliance results to the user. EnergyPlus annual simulations for proposed and code baseline building models, and mechanical equipment sizing result in simulation run times beyond acceptable limits. This paper presents a study that compares the results of a shortened simulation time period using 4 weeks of hourly weather data (one per quarter), to an annual simulation using full 52 weeks of hourly weather data. Three representative building types based on DOE Prototype Building Models and threemore » climate zones were used for determining the validity of using a shortened simulation run period. Further sensitivity analysis and run time comparisons were made to evaluate the robustness and run time savings of using this approach. The results of this analysis show that the shortened simulation run period provides compliance index calculations within 1% of those predicted using annual simulation results, and typically saves about 75% of simulation run time.« less

Parameters that affect parallel processing for computational electromagnetic simulation codes on high performance computing clusters

NASA Astrophysics Data System (ADS)

Moon, Hongsik

What is the impact of multicore and associated advanced technologies on computational software for science? Most researchers and students have multicore laptops or desktops for their research and they need computing power to run computational software packages. Computing power was initially derived from Central Processing Unit (CPU) clock speed. That changed when increases in clock speed became constrained by power requirements. Chip manufacturers turned to multicore CPU architectures and associated technological advancements to create the CPUs for the future. Most software applications benefited by the increased computing power the same way that increases in clock speed helped applications run faster. However, for Computational ElectroMagnetics (CEM) software developers, this change was not an obvious benefit - it appeared to be a detriment. Developers were challenged to find a way to correctly utilize the advancements in hardware so that their codes could benefit. The solution was parallelization and this dissertation details the investigation to address these challenges. Prior to multicore CPUs, advanced computer technologies were compared with the performance using benchmark software and the metric was FLoting-point Operations Per Seconds (FLOPS) which indicates system performance for scientific applications that make heavy use of floating-point calculations. Is FLOPS an effective metric for parallelized CEM simulation tools on new multicore system? Parallel CEM software needs to be benchmarked not only by FLOPS but also by the performance of other parameters related to type and utilization of the hardware, such as CPU, Random Access Memory (RAM), hard disk, network, etc. The codes need to be optimized for more than just FLOPs and new parameters must be included in benchmarking. In this dissertation, the parallel CEM software named High Order Basis Based Integral Equation Solver (HOBBIES) is introduced. This code was developed to address the needs of the changing computer hardware platforms in order to provide fast, accurate and efficient solutions to large, complex electromagnetic problems. The research in this dissertation proves that the performance of parallel code is intimately related to the configuration of the computer hardware and can be maximized for different hardware platforms. To benchmark and optimize the performance of parallel CEM software, a variety of large, complex projects are created and executed on a variety of computer platforms. The computer platforms used in this research are detailed in this dissertation. The projects run as benchmarks are also described in detail and results are presented. The parameters that affect parallel CEM software on High Performance Computing Clusters (HPCC) are investigated. This research demonstrates methods to maximize the performance of parallel CEM software code.

PRay - A graphical user interface for interactive visualization and modification of rayinvr models

NASA Astrophysics Data System (ADS)

Fromm, T.

2016-01-01

PRay is a graphical user interface for interactive displaying and editing of velocity models for seismic refraction. It is optimized for editing rayinvr models but can also be used as a dynamic viewer for ray tracing results from other software. The main features are the graphical editing of nodes and fast adjusting of the display (stations and phases). It can be extended by user-defined shell scripts and links to phase picking software. PRay is open source software written in the scripting language Perl, runs on Unix-like operating systems including Mac OS X and provides a version controlled source code repository for community development (https://sourceforge.net/projects/pray-plot-rayinvr/).

The viability of ADVANTG deterministic method for synthetic radiography generation

NASA Astrophysics Data System (ADS)

Bingham, Andrew; Lee, Hyoung K.

2018-07-01

Fast simulation techniques to generate synthetic radiographic images of high resolution are helpful when new radiation imaging systems are designed. However, the standard stochastic approach requires lengthy run time with poorer statistics at higher resolution. The investigation of the viability of a deterministic approach to synthetic radiography image generation was explored. The aim was to analyze a computational time decrease over the stochastic method. ADVANTG was compared to MCNP in multiple scenarios including a small radiography system prototype, to simulate high resolution radiography images. By using ADVANTG deterministic code to simulate radiography images the computational time was found to decrease 10 to 13 times compared to the MCNP stochastic approach while retaining image quality.

Benchmarking and performance analysis of the CM-2. [SIMD computer

NASA Technical Reports Server (NTRS)

Myers, David W.; Adams, George B., II

1988-01-01

A suite of benchmarking routines testing communication, basic arithmetic operations, and selected kernel algorithms written in LISP and PARIS was developed for the CM-2. Experiment runs are automated via a software framework that sequences individual tests, allowing for unattended overnight operation. Multiple measurements are made and treated statistically to generate well-characterized results from the noisy values given by cm:time. The results obtained provide a comparison with similar, but less extensive, testing done on a CM-1. Tests were chosen to aid the algorithmist in constructing fast, efficient, and correct code on the CM-2, as well as gain insight into what performance criteria are needed when evaluating parallel processing machines.

Neutronic calculation of fast reactors by the EUCLID/V1 integrated code

NASA Astrophysics Data System (ADS)

Koltashev, D. A.; Stakhanova, A. A.

2017-01-01

This article considers neutronic calculation of a fast-neutron lead-cooled reactor BREST-OD-300 by the EUCLID/V1 integrated code. The main goal of development and application of integrated codes is a nuclear power plant safety justification. EUCLID/V1 is integrated code designed for coupled neutronics, thermomechanical and thermohydraulic fast reactor calculations under normal and abnormal operating conditions. EUCLID/V1 code is being developed in the Nuclear Safety Institute of the Russian Academy of Sciences. The integrated code has a modular structure and consists of three main modules: thermohydraulic module HYDRA-IBRAE/LM/V1, thermomechanical module BERKUT and neutronic module DN3D. In addition, the integrated code includes databases with fuel, coolant and structural materials properties. Neutronic module DN3D provides full-scale simulation of neutronic processes in fast reactors. Heat sources distribution, control rods movement, reactivity level changes and other processes can be simulated. Neutron transport equation in multigroup diffusion approximation is solved. This paper contains some calculations implemented as a part of EUCLID/V1 code validation. A fast-neutron lead-cooled reactor BREST-OD-300 transient simulation (fuel assembly floating, decompression of passive feedback system channel) and cross-validation with MCU-FR code results are presented in this paper. The calculations demonstrate EUCLID/V1 code application for BREST-OD-300 simulating and safety justification.

Investigation and Optimization of Blade Tip Winglets Using an Implicit Free Wake Vortex Method

NASA Astrophysics Data System (ADS)

Lawton, Stephen; Crawford, Curran

2014-06-01

Novel outer-blade geometries such as tip winglets can increase the aerodynamic power that can be extracted from the wind by tailoring the relative position and strengths of trailed vorticity. This design space is explored using both parameter studies and gradient-based optimization, with the aerodynamic analysis carried out using LibAero, a free wake vortex-based code introduced in previous work. The starting design is the NREL 5MW reference turbine, which allows comparison of the aerodynamic simulation for the unmodified blade with other codes. The code uses a Prandtl-Weissinger lifting line model to represent the blade, and vortex filaments as the flow elements. A fast multipole method is implemented to accelerate the influence calculations and reduce the computational cost. This results in higher fidelity aerodynamic simulations that can capture the effects of novel geometries while maintaining sufficiently fast run-times (on the order of an hour) to allow the use of optimization. Gradients of the objective function with respect to design variables are calculated using the complex step method which is accurate and efficient. Since the vortex structure behind the rotor is being resolved in detail, insight is also gained into the mechanisms by which these new blade designs affect performance. It is found that adding winglets can increase the power extracted from the wind by around 2%, with a similar increase in thrust. It is also possible to create a winglet that slightly lowers the thrust while maintaining very similar power compared to the standard straight blade.

Deep learning for galaxy surface brightness profile fitting

NASA Astrophysics Data System (ADS)

Tuccillo, D.; Huertas-Company, M.; Decencière, E.; Velasco-Forero, S.; Domínguez Sánchez, H.; Dimauro, P.

2018-03-01

Numerous ongoing and future large area surveys (e.g. Dark Energy Survey, EUCLID, Large Synoptic Survey Telescope, Wide Field Infrared Survey Telescope) will increase by several orders of magnitude the volume of data that can be exploited for galaxy morphology studies. The full potential of these surveys can be unlocked only with the development of automated, fast, and reliable analysis methods. In this paper, we present DeepLeGATo, a new method for 2-D photometric galaxy profile modelling, based on convolutional neural networks. Our code is trained and validated on analytic profiles (HST/CANDELS F160W filter) and it is able to retrieve the full set of parameters of one-component Sérsic models: total magnitude, effective radius, Sérsic index, and axis ratio. We show detailed comparisons between our code and GALFIT. On simulated data, our method is more accurate than GALFIT and ˜3000 time faster on GPU (˜50 times when running on the same CPU). On real data, DeepLeGATo trained on simulations behaves similarly to GALFIT on isolated galaxies. With a fast domain adaptation step made with the 0.1-0.8 per cent the size of the training set, our code is easily capable to reproduce the results obtained with GALFIT even on crowded regions. DeepLeGATo does not require any human intervention beyond the training step, rendering it much automated than traditional profiling methods. The development of this method for more complex models (two-component galaxies, variable point spread function, dense sky regions) could constitute a fundamental tool in the era of big data in astronomy.

"Observation Obscurer" - Time Series Viewer, Editor and Processor

NASA Astrophysics Data System (ADS)

Andronov, I. L.

The program is described, which contains a set of subroutines suitable for East viewing and interactive filtering and processing of regularly and irregularly spaced time series. Being a 32-bit DOS application, it may be used as a default fast viewer/editor of time series in any compute shell ("commander") or in Windows. It allows to view the data in the "time" or "phase" mode, to remove ("obscure") or filter outstanding bad points; to make scale transformations and smoothing using few methods (e.g. mean with phase binning, determination of the statistically opti- mal number of phase bins; "running parabola" (Andronov, 1997, As. Ap. Suppl, 125, 207) fit and to make time series analysis using some methods, e.g. correlation, autocorrelation and histogram analysis: determination of extrema etc. Some features have been developed specially for variable star observers, e.g. the barycentric correction, the creation and fast analysis of "OC" diagrams etc. The manual for "hot keys" is presented. The computer code was compiled with a 32-bit Free Pascal (www.freepascal.org).

Fourier-Bessel Particle-In-Cell (FBPIC) v0.1.0

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

Lehe, Remi; Kirchen, Manuel; Jalas, Soeren

The Fourier-Bessel Particle-In-Cell code is a scientific simulation software for relativistic plasma physics. It is a Particle-In-Cell code whose distinctive feature is to use a spectral decomposition in cylindrical geometry. This decomposition allows to combine the advantages of spectral 3D Cartesian PIC codes (high accuracy and stability) and those of finite-difference cylindrical PIC codes with azimuthal decomposition (orders-of-magnitude speedup when compared to 3D simulations). The code is built on Python and can run both on CPU and GPU (the GPU runs being typically 1 or 2 orders of magnitude faster than the corresponding CPU runs.) The code has the exactmore » same output format as the open-source PIC codes Warp and PIConGPU (openPMD format: openpmd.org) and has a very similar input format as Warp (Python script with many similarities). There is therefore tight interoperability between Warp and FBPIC, and this interoperability will increase even more in the future.« less

Interactive three-dimensional visualization and creation of geometries for Monte Carlo calculations

NASA Astrophysics Data System (ADS)

Theis, C.; Buchegger, K. H.; Brugger, M.; Forkel-Wirth, D.; Roesler, S.; Vincke, H.

2006-06-01

The implementation of three-dimensional geometries for the simulation of radiation transport problems is a very time-consuming task. Each particle transport code supplies its own scripting language and syntax for creating the geometries. All of them are based on the Constructive Solid Geometry scheme requiring textual description. This makes the creation a tedious and error-prone task, which is especially hard to master for novice users. The Monte Carlo code FLUKA comes with built-in support for creating two-dimensional cross-sections through the geometry and FLUKACAD, a custom-built converter to the commercial Computer Aided Design package AutoCAD, exists for 3D visualization. For other codes, like MCNPX, a couple of different tools are available, but they are often specifically tailored to the particle transport code and its approach used for implementing geometries. Complex constructive solid modeling usually requires very fast and expensive special purpose hardware, which is not widely available. In this paper SimpleGeo is presented, which is an implementation of a generic versatile interactive geometry modeler using off-the-shelf hardware. It is running on Windows, with a Linux version currently under preparation. This paper describes its functionality, which allows for rapid interactive visualization as well as generation of three-dimensional geometries, and also discusses critical issues regarding common CAD systems.

The COsmic-ray Soil Moisture Interaction Code (COSMIC) for use in data assimilation

NASA Astrophysics Data System (ADS)

Shuttleworth, J.; Rosolem, R.; Zreda, M.; Franz, T.

2013-08-01

Soil moisture status in land surface models (LSMs) can be updated by assimilating cosmic-ray neutron intensity measured in air above the surface. This requires a fast and accurate model to calculate the neutron intensity from the profiles of soil moisture modeled by the LSM. The existing Monte Carlo N-Particle eXtended (MCNPX) model is sufficiently accurate but too slow to be practical in the context of data assimilation. Consequently an alternative and efficient model is needed which can be calibrated accurately to reproduce the calculations made by MCNPX and used to substitute for MCNPX during data assimilation. This paper describes the construction and calibration of such a model, COsmic-ray Soil Moisture Interaction Code (COSMIC), which is simple, physically based and analytic, and which, because it runs at least 50 000 times faster than MCNPX, is appropriate in data assimilation applications. The model includes simple descriptions of (a) degradation of the incoming high-energy neutron flux with soil depth, (b) creation of fast neutrons at each depth in the soil, and (c) scattering of the resulting fast neutrons before they reach the soil surface, all of which processes may have parameterized dependency on the chemistry and moisture content of the soil. The site-to-site variability in the parameters used in COSMIC is explored for 42 sample sites in the COsmic-ray Soil Moisture Observing System (COSMOS), and the comparative performance of COSMIC relative to MCNPX when applied to represent interactions between cosmic-ray neutrons and moist soil is explored. At an example site in Arizona, fast-neutron counts calculated by COSMIC from the average soil moisture profile given by an independent network of point measurements in the COSMOS probe footprint are similar to the fast-neutron intensity measured by the COSMOS probe. It was demonstrated that, when used within a data assimilation framework to assimilate COSMOS probe counts into the Noah land surface model at the Santa Rita Experimental Range field site, the calibrated COSMIC model provided an effective mechanism for translating model-calculated soil moisture profiles into aboveground fast-neutron count when applied with two radically different approaches used to remove the bias between data and model.

MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit

PubMed Central

Li, Junhua; Chen, Weineng; Chen, Hua; Mende, Daniel R.; Arumugam, Manimozhiyan; Pan, Qi; Liu, Binghang; Qin, Junjie; Wang, Jun; Bork, Peer

2012-01-01

MOCAT is a highly configurable, modular pipeline for fast, standardized processing of single or paired-end sequencing data generated by the Illumina platform. The pipeline uses state-of-the-art programs to quality control, map, and assemble reads from metagenomic samples sequenced at a depth of several billion base pairs, and predict protein-coding genes on assembled metagenomes. Mapping against reference databases allows for read extraction or removal, as well as abundance calculations. Relevant statistics for each processing step can be summarized into multi-sheet Excel documents and queryable SQL databases. MOCAT runs on UNIX machines and integrates seamlessly with the SGE and PBS queuing systems, commonly used to process large datasets. The open source code and modular architecture allow users to modify or exchange the programs that are utilized in the various processing steps. Individual processing steps and parameters were benchmarked and tested on artificial, real, and simulated metagenomes resulting in an improvement of selected quality metrics. MOCAT can be freely downloaded at http://www.bork.embl.de/mocat/. PMID:23082188

Transient Vibration Prediction for Rotors on Ball Bearings Using Load-dependent Non-linear Bearing Stiffness

NASA Technical Reports Server (NTRS)

Fleming, David P.; Poplawski, J. V.

2002-01-01

Rolling-element bearing forces vary nonlinearly with bearing deflection. Thus an accurate rotordynamic transient analysis requires bearing forces to be determined at each step of the transient solution. Analyses have been carried out to show the effect of accurate bearing transient forces (accounting for non-linear speed and load dependent bearing stiffness) as compared to conventional use of average rolling-element bearing stiffness. Bearing forces were calculated by COBRA-AHS (Computer Optimized Ball and Roller Bearing Analysis - Advanced High Speed) and supplied to the rotordynamics code ARDS (Analysis of Rotor Dynamic Systems) for accurate simulation of rotor transient behavior. COBRA-AHS is a fast-running 5 degree-of-freedom computer code able to calculate high speed rolling-element bearing load-displacement data for radial and angular contact ball bearings and also for cylindrical and tapered roller beatings. Results show that use of nonlinear bearing characteristics is essential for accurate prediction of rotordynamic behavior.

Multicore-based 3D-DWT video encoder

NASA Astrophysics Data System (ADS)

Galiano, Vicente; López-Granado, Otoniel; Malumbres, Manuel P.; Migallón, Hector

2013-12-01

Three-dimensional wavelet transform (3D-DWT) encoders are good candidates for applications like professional video editing, video surveillance, multi-spectral satellite imaging, etc. where a frame must be reconstructed as quickly as possible. In this paper, we present a new 3D-DWT video encoder based on a fast run-length coding engine. Furthermore, we present several multicore optimizations to speed-up the 3D-DWT computation. An exhaustive evaluation of the proposed encoder (3D-GOP-RL) has been performed, and we have compared the evaluation results with other video encoders in terms of rate/distortion (R/D), coding/decoding delay, and memory consumption. Results show that the proposed encoder obtains good R/D results for high-resolution video sequences with nearly in-place computation using only the memory needed to store a group of pictures. After applying the multicore optimization strategies over the 3D DWT, the proposed encoder is able to compress a full high-definition video sequence in real-time.

Software design and implementation of ship heave motion monitoring system based on MBD method

NASA Astrophysics Data System (ADS)

Yu, Yan; Li, Yuhan; Zhang, Chunwei; Kang, Won-Hee; Ou, Jinping

2015-03-01

Marine transportation plays a significant role in the modern transport sector due to its advantage of low cost, large capacity. It is being attached enormous importance to all over the world. Nowadays the related areas of product development have become an existing hot spot. DSP signal processors feature micro volume, low cost, high precision, fast processing speed, which has been widely used in all kinds of monitoring systems. But traditional DSP code development process is time-consuming, inefficiency, costly and difficult. MathWorks company proposed Model-based Design (MBD) to overcome these defects. By calling the target board modules in simulink library to compile and generate the corresponding code for the target processor. And then automatically call DSP integrated development environment CCS for algorithm validation on the target processor. This paper uses the MDB to design the algorithm for the ship heave motion monitoring system. It proves the effectiveness of the MBD run successfully on the processor.

MOCAT: a metagenomics assembly and gene prediction toolkit.

PubMed

Kultima, Jens Roat; Sunagawa, Shinichi; Li, Junhua; Chen, Weineng; Chen, Hua; Mende, Daniel R; Arumugam, Manimozhiyan; Pan, Qi; Liu, Binghang; Qin, Junjie; Wang, Jun; Bork, Peer

2012-01-01

MOCAT is a highly configurable, modular pipeline for fast, standardized processing of single or paired-end sequencing data generated by the Illumina platform. The pipeline uses state-of-the-art programs to quality control, map, and assemble reads from metagenomic samples sequenced at a depth of several billion base pairs, and predict protein-coding genes on assembled metagenomes. Mapping against reference databases allows for read extraction or removal, as well as abundance calculations. Relevant statistics for each processing step can be summarized into multi-sheet Excel documents and queryable SQL databases. MOCAT runs on UNIX machines and integrates seamlessly with the SGE and PBS queuing systems, commonly used to process large datasets. The open source code and modular architecture allow users to modify or exchange the programs that are utilized in the various processing steps. Individual processing steps and parameters were benchmarked and tested on artificial, real, and simulated metagenomes resulting in an improvement of selected quality metrics. MOCAT can be freely downloaded at http://www.bork.embl.de/mocat/.

TORBEAM 2.0, a paraxial beam tracing code for electron-cyclotron beams in fusion plasmas for extended physics applications

NASA Astrophysics Data System (ADS)

Poli, E.; Bock, A.; Lochbrunner, M.; Maj, O.; Reich, M.; Snicker, A.; Stegmeir, A.; Volpe, F.; Bertelli, N.; Bilato, R.; Conway, G. D.; Farina, D.; Felici, F.; Figini, L.; Fischer, R.; Galperti, C.; Happel, T.; Lin-Liu, Y. R.; Marushchenko, N. B.; Mszanowski, U.; Poli, F. M.; Stober, J.; Westerhof, E.; Zille, R.; Peeters, A. G.; Pereverzev, G. V.

2018-04-01

The paraxial WKB code TORBEAM (Poli, 2001) is widely used for the description of electron-cyclotron waves in fusion plasmas, retaining diffraction effects through the solution of a set of ordinary differential equations. With respect to its original form, the code has undergone significant transformations and extensions, in terms of both the physical model and the spectrum of applications. The code has been rewritten in Fortran 90 and transformed into a library, which can be called from within different (not necessarily Fortran-based) workflows. The models for both absorption and current drive have been extended, including e.g. fully-relativistic calculation of the absorption coefficient, momentum conservation in electron-electron collisions and the contribution of more than one harmonic to current drive. The code can be run also for reflectometry applications, with relativistic corrections for the electron mass. Formulas that provide the coupling between the reflected beam and the receiver have been developed. Accelerated versions of the code are available, with the reduced physics goal of inferring the location of maximum absorption (including or not the total driven current) for a given setting of the launcher mirrors. Optionally, plasma volumes within given flux surfaces and corresponding values of minimum and maximum magnetic field can be provided externally to speed up the calculation of full driven-current profiles. These can be employed in real-time control algorithms or for fast data analysis.

Designing and Implementing an OVERFLOW Reader for ParaView and Comparing Performance Between Central Processing Units and Graphical Processing Units

NASA Technical Reports Server (NTRS)

Chawner, David M.; Gomez, Ray J.

2010-01-01

In the Applied Aerosciences and CFD branch at Johnson Space Center, computational simulations are run that face many challenges. Two of which are the ability to customize software for specialized needs and the need to run simulations as fast as possible. There are many different tools that are used for running these simulations and each one has its own pros and cons. Once these simulations are run, there needs to be software capable of visualizing the results in an appealing manner. Some of this software is called open source, meaning that anyone can edit the source code to make modifications and distribute it to all other users in a future release. This is very useful, especially in this branch where many different tools are being used. File readers can be written to load any file format into a program, to ease the bridging from one tool to another. Programming such a reader requires knowledge of the file format that is being read as well as the equations necessary to obtain the derived values after loading. When running these CFD simulations, extremely large files are being loaded and having values being calculated. These simulations usually take a few hours to complete, even on the fastest machines. Graphics processing units (GPUs) are usually used to load the graphics for computers; however, in recent years, GPUs are being used for more generic applications because of the speed of these processors. Applications run on GPUs have been known to run up to forty times faster than they would on normal central processing units (CPUs). If these CFD programs are extended to run on GPUs, the amount of time they would require to complete would be much less. This would allow more simulations to be run in the same amount of time and possibly perform more complex computations.

Transit shapes and self-organizing maps as a tool for ranking planetary candidates: application to Kepler and K2

NASA Astrophysics Data System (ADS)

Armstrong, D. J.; Pollacco, D.; Santerne, A.

2017-03-01

A crucial step in planet hunting surveys is to select the best candidates for follow-up observations, given limited telescope resources. This is often performed by human 'eyeballing', a time consuming and statistically awkward process. Here, we present a new, fast machine learning technique to separate true planet signals from astrophysical false positives. We use self-organizing maps (SOMs) to study the transit shapes of Kepler and K2 known and candidate planets. We find that SOMs are capable of distinguishing known planets from known false positives with a success rate of 87.0 per cent, using the transit shape alone. Furthermore, they do not require any candidate to be dispositioned prior to use, meaning that they can be used early in a mission's lifetime. A method for classifying candidates using a SOM is developed, and applied to previously unclassified members of the Kepler Objects of Interest (KOI) list as well as candidates from the K2 mission. The method is extremely fast, taking minutes to run the entire KOI list on a typical laptop. We make PYTHON code for performing classifications publicly available, using either new SOMs or those created in this work. The SOM technique represents a novel method for ranking planetary candidate lists, and can be used both alone or as part of a larger autovetting code.

Propulsion strategy in the gait of primary school children; the effect of age and speed.

PubMed

Lye, Jillian; Parkinson, Stephanie; Diamond, Nicola; Downs, Jenny; Morris, Susan

2016-12-01

The strategy used to generate power for forward propulsion in walking and running has recently been highlighted as a marker of gait maturation and elastic energy recycling. This study investigated ankle and hip power generation as a propulsion strategy (PS) during the late stance/early swing phases of walking and running in typically developing (TD) children (15: six to nine years; 17: nine to 13years) using three-dimensional gait analysis. Peak ankle power generation at push-off (peakA2), peak hip power generation in early swing (peakH3) and propulsion strategy (PS) [peakA2/(peakA2+peakH3)] were calculated to provide the relative contribution of ankle power to total propulsion. Mean PS values decreased as speed increased for comfortable walking (p<0.001), fast walking (p<0.001) and fast running (p<0.001), and less consistently during jogging (p=0.054). PS varied with age (p<0.001) only during fast walking. At any speed of fast walking, older children generated more peakA2 (p=0.001) and less peakH3 (p=0.001) than younger children. While the kinetics of running propulsion appear to be developed by age six years, the skills of fast walking appeared to require additional neuromuscular maturity. These findings support the concept that running is a skill that matures early for TD children. Copyright © 2016 Elsevier B.V. All rights reserved.

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.

Voltage linear transformation circuit design

NASA Astrophysics Data System (ADS)

Sanchez, Lucas R. W.; Jin, Moon-Seob; Scott, R. Phillip; Luder, Ryan J.; Hart, Michael

2017-09-01

Many engineering projects require automated control of analog voltages over a specified range. We have developed a computer interface comprising custom hardware and MATLAB code to provide real-time control of a Thorlabs adaptive optics (AO) kit. The hardware interface includes an op amp cascade to linearly shift and scale a voltage range. With easy modifications, any linear transformation can be accommodated. In AO applications, the design is suitable to drive a range of different types of deformable and fast steering mirrors (FSM's). Our original motivation and application was to control an Optics in Motion (OIM) FSM which requires the customer to devise a unique interface to supply voltages to the mirror controller to set the mirror's angular deflection. The FSM is in an optical servo loop with a wave front sensor (WFS), which controls the dynamic behavior of the mirror's deflection. The code acquires wavefront data from the WFS and fits a plane, which is subsequently converted into its corresponding angular deflection. The FSM provides +/-3° optical angular deflection for a +/-10 V voltage swing. Voltages are applied to the mirror via a National Instruments digital-to-analog converter (DAC) followed by an op amp cascade circuit. This system has been integrated into our Thorlabs AO testbed which currently runs at 11 Hz, but with planned software upgrades, the system update rate is expected to improve to 500 Hz. To show that the FSM subsystem is ready for this speed, we conducted two different PID tuning runs at different step commands. Once 500 Hz is achieved, we plan to make the code and method for our interface solution freely available to the community.

Positional demands of international rugby union: evaluation of player actions and movements.

PubMed

Quarrie, Kenneth L; Hopkins, Will G; Anthony, Mike J; Gill, Nicholas D

2013-07-01

In rugby union, published analyses of actions and movements of players during matches have been limited to small samples of games at regional or national level. To analyse movements and activities of players in international rugby union matches with a sample size sufficient to clearly delineate positional roles. Observational study. Actions of 763 players were coded from video recordings of 90 international matches played by the New Zealand national team (the All Blacks) from 2004 to 2010. Movements of players were coded for 27 of these matches via a semi-automated player-tracking system. Movements and activities of all players from both teams were coded. Cluster analysis of activities and time-motion variables produced five subgroups of forwards (props, hookers, locks, flankers, Number 8 forwards) and five subgroups of backs (scrum-half, fly-half, midfield backs, wings and fullbacks). Forwards sustained much higher contact loads per match than backs, via scrums, rucks, tackles and mauls. Mean distance covered per match ranged from 5400 to 6300m, with backs generally running further than forwards. There were marked differences between positional groups in the amount of distance covered at various speeds. The amount of play per match varies by position due to differences in rates at which players are substituted. The distance covered by players at relatively fast running speeds (in excess of 5ms(-1)) appears to be higher during international matches than when competing at lower levels of the professional game. The specific match demands for positional groups need to be considered when managing player workloads. Copyright © 2012 Sports Medicine Australia. Published by Elsevier Ltd. All rights reserved.

Shear-wave velocity model from Rayleigh wave group velocities centered on the Sacramento/San Joaquin Delta

USGS Publications Warehouse

Fletcher, Jon Peter B.; Erdem, Jemile

2017-01-01

Rayleigh wave group velocities obtained from ambient noise tomography are inverted for an upper crustal model of the Central Valley, California, centered on the Sacramento/San Joaquin Delta. Two methods were tried; the first uses SURF96, a least-squares routine. It provides a good fit to the data, but convergence is dependent on the starting model. The second uses a genetic algorithm, whose starting model is random. This method was tried at several nodes in the model and compared to the output from SURF96. The genetic code is run five times and the variance of the output of all five models can be used to obtain an estimate of error. SURF96 produces a more regular solution mostly because it is typically run with a smoothing constraint. Models from the genetic code are generally consistent with the SURF96 code sometimes producing lower velocities at depth. The full model, calculated using SURF96, employed a 2-pass strategy, which used a variable damping scheme in the first pass. The resulting model shows low velocities near the surface in the Central Valley with a broad asymmetrical sedimentary basin located close to the western edge of the Central Valley near 122°W longitude. At shallow depths the Rio Vista Basin is found nestled between the Pittsburgh/Kirby Hills and Midland faults, but a significant basin also seems to exist to the west of the Kirby Hills fault. There are other possible correlations between fast and slow velocities in the Central Valley and geologic features such as the Stockton Arch, oil or gas producing regions and the fault-controlled western boundary of the Central Valley.

Shear-wave Velocity Model from Rayleigh Wave Group Velocities Centered on the Sacramento/San Joaquin Delta

NASA Astrophysics Data System (ADS)

Fletcher, Jon B.; Erdem, Jemile

2017-10-01

Rayleigh wave group velocities obtained from ambient noise tomography are inverted for an upper crustal model of the Central Valley, California, centered on the Sacramento/San Joaquin Delta. Two methods were tried; the first uses SURF96, a least squares routine. It provides a good fit to the data, but convergence is dependent on the starting model. The second uses a genetic algorithm, whose starting model is random. This method was tried at several nodes in the model and compared to the output from SURF96. The genetic code is run five times and the variance of the output of all five models can be used to obtain an estimate of error. SURF96 produces a more regular solution mostly because it is typically run with a smoothing constraint. Models from the genetic code are generally consistent with the SURF96 code sometimes producing lower velocities at depth. The full model, calculated using SURF96, employed a 2-pass strategy, which used a variable damping scheme in the first pass. The resulting model shows low velocities near the surface in the Central Valley with a broad asymmetrical sedimentary basin located close to the western edge of the Central Valley near 122°W longitude. At shallow depths, the Rio Vista Basin is found nestled between the Pittsburgh/Kirby Hills and Midland faults, but a significant basin also seems to exist to the west of the Kirby Hills fault. There are other possible correlations between fast and slow velocities in the Central Valley and geologic features such as the Stockton Arch, oil or gas producing regions and the fault-controlled western boundary of the Central Valley.

Applications Performance Under MPL and MPI on NAS IBM SP2

NASA Technical Reports Server (NTRS)

Saini, Subhash; Simon, Horst D.; Lasinski, T. A. (Technical Monitor)

1994-01-01

On July 5, 1994, an IBM Scalable POWER parallel System (IBM SP2) with 64 nodes, was installed at the Numerical Aerodynamic Simulation (NAS) Facility Each node of NAS IBM SP2 is a "wide node" consisting of a RISC 6000/590 workstation module with a clock of 66.5 MHz which can perform four floating point operations per clock with a peak performance of 266 Mflop/s. By the end of 1994, 64 nodes of IBM SP2 will be upgraded to 160 nodes with a peak performance of 42.5 Gflop/s. An overview of the IBM SP2 hardware is presented. The basic understanding of architectural details of RS 6000/590 will help application scientists the porting, optimizing, and tuning of codes from other machines such as the CRAY C90 and the Paragon to the NAS SP2. Optimization techniques such as quad-word loading, effective utilization of two floating point units, and data cache optimization of RS 6000/590 is illustrated, with examples giving performance gains at each optimization step. The conversion of codes using Intel's message passing library NX to codes using native Message Passing Library (MPL) and the Message Passing Interface (NMI) library available on the IBM SP2 is illustrated. In particular, we will present the performance of Fast Fourier Transform (FFT) kernel from NAS Parallel Benchmarks (NPB) under MPL and MPI. We have also optimized some of Fortran BLAS 2 and BLAS 3 routines, e.g., the optimized Fortran DAXPY runs at 175 Mflop/s and optimized Fortran DGEMM runs at 230 Mflop/s per node. The performance of the NPB (Class B) on the IBM SP2 is compared with the CRAY C90, Intel Paragon, TMC CM-5E, and the CRAY T3D.

The Monte Carlo photoionization and moving-mesh radiation hydrodynamics code CMACIONIZE

NASA Astrophysics Data System (ADS)

Vandenbroucke, B.; Wood, K.

2018-04-01

We present the public Monte Carlo photoionization and moving-mesh radiation hydrodynamics code CMACIONIZE, which can be used to simulate the self-consistent evolution of HII regions surrounding young O and B stars, or other sources of ionizing radiation. The code combines a Monte Carlo photoionization algorithm that uses a complex mix of hydrogen, helium and several coolants in order to self-consistently solve for the ionization and temperature balance at any given type, with a standard first order hydrodynamics scheme. The code can be run as a post-processing tool to get the line emission from an existing simulation snapshot, but can also be used to run full radiation hydrodynamical simulations. Both the radiation transfer and the hydrodynamics are implemented in a general way that is independent of the grid structure that is used to discretize the system, allowing it to be run both as a standard fixed grid code, but also as a moving-mesh code.

Health and nutrition content claims on Australian fast-food websites.

PubMed

Wellard, Lyndal; Koukoumas, Alexandra; Watson, Wendy L; Hughes, Clare

2017-03-01

To determine the extent that Australian fast-food websites contain nutrition content and health claims, and whether these claims are compliant with the new provisions of the Australia New Zealand Food Standards Code ('the Code'). Systematic content analysis of all web pages to identify nutrition content and health claims. Nutrition information panels were used to determine whether products with claims met Nutrient Profiling Scoring Criteria (NPSC) and qualifying criteria, and to compare them with the Code to determine compliance. Australian websites of forty-four fast-food chains including meals, bakery, ice cream, beverage and salad chains. Any products marketed on the websites using health or nutrition content claims. Of the forty-four fast-food websites, twenty (45 %) had at least one claim. A total of 2094 claims were identified on 371 products, including 1515 nutrition content (72 %) and 579 health claims (28 %). Five fast-food products with health (5 %) and 157 products with nutrition content claims (43 %) did not meet the requirements of the Code to allow them to carry such claims. New provisions in the Code came into effect in January 2016 after a 3-year transition. Food regulatory agencies should review fast-food websites to ensure compliance with the qualifying criteria for nutrition content and health claim regulations. This would prevent consumers from viewing unhealthy foods as healthier choices. Healthy choices could be facilitated by applying NPSC to nutrition content claims. Fast-food chains should be educated on the requirements of the Code regarding claims.

Fast-SNP: a fast matrix pre-processing algorithm for efficient loopless flux optimization of metabolic models

PubMed Central

Saa, Pedro A.; Nielsen, Lars K.

2016-01-01

Motivation: Computation of steady-state flux solutions in large metabolic models is routinely performed using flux balance analysis based on a simple LP (Linear Programming) formulation. A minimal requirement for thermodynamic feasibility of the flux solution is the absence of internal loops, which are enforced using ‘loopless constraints’. The resulting loopless flux problem is a substantially harder MILP (Mixed Integer Linear Programming) problem, which is computationally expensive for large metabolic models. Results: We developed a pre-processing algorithm that significantly reduces the size of the original loopless problem into an easier and equivalent MILP problem. The pre-processing step employs a fast matrix sparsification algorithm—Fast- sparse null-space pursuit (SNP)—inspired by recent results on SNP. By finding a reduced feasible ‘loop-law’ matrix subject to known directionalities, Fast-SNP considerably improves the computational efficiency in several metabolic models running different loopless optimization problems. Furthermore, analysis of the topology encoded in the reduced loop matrix enabled identification of key directional constraints for the potential permanent elimination of infeasible loops in the underlying model. Overall, Fast-SNP is an effective and simple algorithm for efficient formulation of loop-law constraints, making loopless flux optimization feasible and numerically tractable at large scale. Availability and Implementation: Source code for MATLAB including examples is freely available for download at http://www.aibn.uq.edu.au/cssb-resources under Software. Optimization uses Gurobi, CPLEX or GLPK (the latter is included with the algorithm). Contact: lars.nielsen@uq.edu.au Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27559155

Analytic barrage attack model. Final report, January 1986-January 1989

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

St Ledger, J.W.; Naegeli, R.E.; Dowden, N.A.

An analytic model is developed for a nuclear barrage attack, assuming weapons with no aiming error and a cookie-cutter damage function. The model is then extended with approximations for the effects of aiming error and distance damage sigma. The final result is a fast running model which calculates probability of damage for a barrage attack. The probability of damage is accurate to within seven percent or better, for weapon reliabilities of 50 to 100 percent, distance damage sigmas of 0.5 or less, and zero to very large circular error probabilities. FORTRAN 77 coding is included in the report for themore » analytic model and for a numerical model used to check the analytic results.« less

An Optical Model for Estimating the Underwater Light Field from Remote Sensing

NASA Technical Reports Server (NTRS)

Liu, Cheng-Chien; Miller, Richard L.

2002-01-01

A model of the wavelength-integrated scalar irradiance for a vertically homogeneous water column is developed. It runs twenty thousand times faster than simulations obtained using full Hydrolight code and limits the percentage error to less than 3.7%. Both the distribution of incident sky radiance and a wind-roughened surface are integrated in the model. Our model removes common limitations of earlier models and can be applied to waters with any composition of the inherent optical properties. Implementation of this new model, as well as the ancillary information required for processing global-scale satellite data, is discussed. This new model is fast, accurate, and flexible and therefore provides important information of the underwater light field from remote sensing.

A GPU OpenCL based cross-platform Monte Carlo dose calculation engine (goMC)

NASA Astrophysics Data System (ADS)

Tian, Zhen; Shi, Feng; Folkerts, Michael; Qin, Nan; Jiang, Steve B.; Jia, Xun

2015-09-01

Monte Carlo (MC) simulation has been recognized as the most accurate dose calculation method for radiotherapy. However, the extremely long computation time impedes its clinical application. Recently, a lot of effort has been made to realize fast MC dose calculation on graphic processing units (GPUs). However, most of the GPU-based MC dose engines have been developed under NVidia’s CUDA environment. This limits the code portability to other platforms, hindering the introduction of GPU-based MC simulations to clinical practice. The objective of this paper is to develop a GPU OpenCL based cross-platform MC dose engine named goMC with coupled photon-electron simulation for external photon and electron radiotherapy in the MeV energy range. Compared to our previously developed GPU-based MC code named gDPM (Jia et al 2012 Phys. Med. Biol. 57 7783-97), goMC has two major differences. First, it was developed under the OpenCL environment for high code portability and hence could be run not only on different GPU cards but also on CPU platforms. Second, we adopted the electron transport model used in EGSnrc MC package and PENELOPE’s random hinge method in our new dose engine, instead of the dose planning method employed in gDPM. Dose distributions were calculated for a 15 MeV electron beam and a 6 MV photon beam in a homogenous water phantom, a water-bone-lung-water slab phantom and a half-slab phantom. Satisfactory agreement between the two MC dose engines goMC and gDPM was observed in all cases. The average dose differences in the regions that received a dose higher than 10% of the maximum dose were 0.48-0.53% for the electron beam cases and 0.15-0.17% for the photon beam cases. In terms of efficiency, goMC was ~4-16% slower than gDPM when running on the same NVidia TITAN card for all the cases we tested, due to both the different electron transport models and the different development environments. The code portability of our new dose engine goMC was validated by successfully running it on a variety of different computing devices including an NVidia GPU card, two AMD GPU cards and an Intel CPU processor. Computational efficiency among these platforms was compared.

A GPU OpenCL based cross-platform Monte Carlo dose calculation engine (goMC).

PubMed

Tian, Zhen; Shi, Feng; Folkerts, Michael; Qin, Nan; Jiang, Steve B; Jia, Xun

2015-10-07

Monte Carlo (MC) simulation has been recognized as the most accurate dose calculation method for radiotherapy. However, the extremely long computation time impedes its clinical application. Recently, a lot of effort has been made to realize fast MC dose calculation on graphic processing units (GPUs). However, most of the GPU-based MC dose engines have been developed under NVidia's CUDA environment. This limits the code portability to other platforms, hindering the introduction of GPU-based MC simulations to clinical practice. The objective of this paper is to develop a GPU OpenCL based cross-platform MC dose engine named goMC with coupled photon-electron simulation for external photon and electron radiotherapy in the MeV energy range. Compared to our previously developed GPU-based MC code named gDPM (Jia et al 2012 Phys. Med. Biol. 57 7783-97), goMC has two major differences. First, it was developed under the OpenCL environment for high code portability and hence could be run not only on different GPU cards but also on CPU platforms. Second, we adopted the electron transport model used in EGSnrc MC package and PENELOPE's random hinge method in our new dose engine, instead of the dose planning method employed in gDPM. Dose distributions were calculated for a 15 MeV electron beam and a 6 MV photon beam in a homogenous water phantom, a water-bone-lung-water slab phantom and a half-slab phantom. Satisfactory agreement between the two MC dose engines goMC and gDPM was observed in all cases. The average dose differences in the regions that received a dose higher than 10% of the maximum dose were 0.48-0.53% for the electron beam cases and 0.15-0.17% for the photon beam cases. In terms of efficiency, goMC was ~4-16% slower than gDPM when running on the same NVidia TITAN card for all the cases we tested, due to both the different electron transport models and the different development environments. The code portability of our new dose engine goMC was validated by successfully running it on a variety of different computing devices including an NVidia GPU card, two AMD GPU cards and an Intel CPU processor. Computational efficiency among these platforms was compared.

Fast transform decoding of nonsystematic Reed-Solomon codes

NASA Technical Reports Server (NTRS)

Truong, T. K.; Cheung, K.-M.; Reed, I. S.; Shiozaki, A.

1989-01-01

A Reed-Solomon (RS) code is considered to be a special case of a redundant residue polynomial (RRP) code, and a fast transform decoding algorithm to correct both errors and erasures is presented. This decoding scheme is an improvement of the decoding algorithm for the RRP code suggested by Shiozaki and Nishida, and can be realized readily on very large scale integration chips.

The mass storage testing laboratory at GSFC

NASA Technical Reports Server (NTRS)

Venkataraman, Ravi; Williams, Joel; Michaud, David; Gu, Heng; Kalluri, Atri; Hariharan, P. C.; Kobler, Ben; Behnke, Jeanne; Peavey, Bernard

1998-01-01

Industry-wide benchmarks exist for measuring the performance of processors (SPECmarks), and of database systems (Transaction Processing Council). Despite storage having become the dominant item in computing and IT (Information Technology) budgets, no such common benchmark is available in the mass storage field. Vendors and consultants provide services and tools for capacity planning and sizing, but these do not account for the complete set of metrics needed in today's archives. The availability of automated tape libraries, high-capacity RAID systems, and high- bandwidth interconnectivity between processor and peripherals has led to demands for services which traditional file systems cannot provide. File Storage and Management Systems (FSMS), which began to be marketed in the late 80's, have helped to some extent with large tape libraries, but their use has introduced additional parameters affecting performance. The aim of the Mass Storage Test Laboratory (MSTL) at Goddard Space Flight Center is to develop a test suite that includes not only a comprehensive check list to document a mass storage environment but also benchmark code. Benchmark code is being tested which will provide measurements for both baseline systems, i.e. applications interacting with peripherals through the operating system services, and for combinations involving an FSMS. The benchmarks are written in C, and are easily portable. They are initially being aimed at the UNIX Open Systems world. Measurements are being made using a Sun Ultra 170 Sparc with 256MB memory running Solaris 2.5.1 with the following configuration: 4mm tape stacker on SCSI 2 Fast/Wide; 4GB disk device on SCSI 2 Fast/Wide; and Sony Petaserve on Fast/Wide differential SCSI 2.

The Scylla Multi-Code Comparison Project

NASA Astrophysics Data System (ADS)

Maller, Ariyeh; Stewart, Kyle; Bullock, James; Oñorbe, Jose; Scylla Team

2016-01-01

Cosmological hydrodynamical simulations are one of the main techniques used to understand galaxy formation and evolution. However, it is far from clear to what extent different numerical techniques and different implementations of feedback yield different results. The Scylla Multi-Code Comparison Project seeks to address this issue by running idenitical initial condition simulations with different popular hydrodynamic galaxy formation codes. Here we compare simulations of a Milky Way mass halo using the codes enzo, ramses, art, arepo and gizmo-psph. The different runs produce galaxies with a variety of properties. There are many differences, but also many similarities. For example we find that in all runs cold flow disks exist; extended gas structures, far beyond the galactic disk, that show signs of rotation. Also, the angular momentum of warm gas in the halo is much larger than the angular momentum of the dark matter. We also find notable differences between runs. The temperature and density distribution of hot gas can differ by over an order of magnitude between codes and the stellar mass to halo mass relation also varies widely. These results suggest that observations of galaxy gas halos and the stellar mass to halo mass relation can be used to constarin the correct model of feedback.

A Validation and Code-to-Code Verification of FAST for a Megawatt-Scale Wind Turbine with Aeroelastically Tailored Blades

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

Guntur, Srinivas; Jonkman, Jason; Sievers, Ryan

This paper presents validation and code-to-code verification of the latest version of the U.S. Department of Energy, National Renewable Energy Laboratory wind turbine aeroelastic engineering simulation tool, FAST v8. A set of 1,141 test cases, for which experimental data from a Siemens 2.3 MW machine have been made available and were in accordance with the International Electrotechnical Commission 61400-13 guidelines, were identified. These conditions were simulated using FAST as well as the Siemens in-house aeroelastic code, BHawC. This paper presents a detailed analysis comparing results from FAST with those from BHawC as well as experimental measurements, using statistics including themore » means and the standard deviations along with the power spectral densities of select turbine parameters and loads. Results indicate a good agreement among the predictions using FAST, BHawC, and experimental measurements. Here, these agreements are discussed in detail in this paper, along with some comments regarding the differences seen in these comparisons relative to the inherent uncertainties in such a model-based analysis.« less

A Validation and Code-to-Code Verification of FAST for a Megawatt-Scale Wind Turbine with Aeroelastically Tailored Blades

DOE PAGES

Guntur, Srinivas; Jonkman, Jason; Sievers, Ryan; ...

2017-08-29

This paper presents validation and code-to-code verification of the latest version of the U.S. Department of Energy, National Renewable Energy Laboratory wind turbine aeroelastic engineering simulation tool, FAST v8. A set of 1,141 test cases, for which experimental data from a Siemens 2.3 MW machine have been made available and were in accordance with the International Electrotechnical Commission 61400-13 guidelines, were identified. These conditions were simulated using FAST as well as the Siemens in-house aeroelastic code, BHawC. This paper presents a detailed analysis comparing results from FAST with those from BHawC as well as experimental measurements, using statistics including themore » means and the standard deviations along with the power spectral densities of select turbine parameters and loads. Results indicate a good agreement among the predictions using FAST, BHawC, and experimental measurements. Here, these agreements are discussed in detail in this paper, along with some comments regarding the differences seen in these comparisons relative to the inherent uncertainties in such a model-based analysis.« less

The Arrow of Time in the Collapse of Collisionless Self-gravitating Systems: Non-validity of the Vlasov-Poisson Equation during Violent Relaxation

NASA Astrophysics Data System (ADS)

Beraldo e Silva, Leandro; de Siqueira Pedra, Walter; Sodré, Laerte; Perico, Eder L. D.; Lima, Marcos

2017-09-01

The collapse of a collisionless self-gravitating system, with the fast achievement of a quasi-stationary state, is driven by violent relaxation, with a typical particle interacting with the time-changing collective potential. It is traditionally assumed that this evolution is governed by the Vlasov-Poisson equation, in which case entropy must be conserved. We run N-body simulations of isolated self-gravitating systems, using three simulation codes, NBODY-6 (direct summation without softening), NBODY-2 (direct summation with softening), and GADGET-2 (tree code with softening), for different numbers of particles and initial conditions. At each snapshot, we estimate the Shannon entropy of the distribution function with three different techniques: Kernel, Nearest Neighbor, and EnBiD. For all simulation codes and estimators, the entropy evolution converges to the same limit as N increases. During violent relaxation, the entropy has a fast increase followed by damping oscillations, indicating that violent relaxation must be described by a kinetic equation other than the Vlasov-Poisson equation, even for N as large as that of astronomical structures. This indicates that violent relaxation cannot be described by a time-reversible equation, shedding some light on the so-called “fundamental paradox of stellar dynamics.” The long-term evolution is well-described by the orbit-averaged Fokker-Planck model, with Coulomb logarithm values in the expected range 10{--}12. By means of NBODY-2, we also study the dependence of the two-body relaxation timescale on the softening length. The approach presented in the current work can potentially provide a general method for testing any kinetic equation intended to describe the macroscopic evolution of N-body systems.

RunJumpCode: An Educational Game for Educating Programming

ERIC Educational Resources Information Center

Hinds, Matthew; Baghaei, Nilufar; Ragon, Pedrito; Lambert, Jonathon; Rajakaruna, Tharindu; Houghton, Travers; Dacey, Simon

2017-01-01

Programming promotes critical thinking, problem solving and analytic skills through creating solutions that can solve everyday problems. However, learning programming can be a daunting experience for a lot of students. "RunJumpCode" is an educational 2D platformer video game, designed and developed in Unity, to teach players the…

Adaptive Grid Refinement for Atmospheric Boundary Layer Simulations

NASA Astrophysics Data System (ADS)

van Hooft, Antoon; van Heerwaarden, Chiel; Popinet, Stephane; van der linden, Steven; de Roode, Stephan; van de Wiel, Bas

2017-04-01

We validate and benchmark an adaptive mesh refinement (AMR) algorithm for numerical simulations of the atmospheric boundary layer (ABL). The AMR technique aims to distribute the computational resources efficiently over a domain by refining and coarsening the numerical grid locally and in time. This can be beneficial for studying cases in which length scales vary significantly in time and space. We present the results for a case describing the growth and decay of a convective boundary layer. The AMR results are benchmarked against two runs using a fixed, fine meshed grid. First, with the same numerical formulation as the AMR-code and second, with a code dedicated to ABL studies. Compared to the fixed and isotropic grid runs, the AMR algorithm can coarsen and refine the grid such that accurate results are obtained whilst using only a fraction of the grid cells. Performance wise, the AMR run was cheaper than the fixed and isotropic grid run with similar numerical formulations. However, for this specific case, the dedicated code outperformed both aforementioned runs.

BISON and MARMOT Development for Modeling Fast Reactor Fuel Performance

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

Gamble, Kyle Allan Lawrence; Williamson, Richard L.; Schwen, Daniel

2015-09-01

BISON and MARMOT are two codes under development at the Idaho National Laboratory for engineering scale and lower length scale fuel performance modeling. It is desired to add capabilities for fast reactor applications to these codes. The fast reactor fuel types under consideration are metal (U-Pu-Zr) and oxide (MOX). The cladding types of interest include 316SS, D9, and HT9. The purpose of this report is to outline the proposed plans for code development and provide an overview of the models added to the BISON and MARMOT codes for fast reactor fuel behavior. A brief overview of preliminary discussions on themore » formation of a bilateral agreement between the Idaho National Laboratory and the National Nuclear Laboratory in the United Kingdom is presented.« less

Fast 2D FWI on a multi and many-cores workstation.

NASA Astrophysics Data System (ADS)

Thierry, Philippe; Donno, Daniela; Noble, Mark

2014-05-01

Following the introduction of x86 co-processors (Xeon Phi) and the performance increase of standard 2-socket workstations using the latest 12 cores E5-v2 x86-64 CPU, we present here a MPI + OpenMP implementation of an acoustic 2D FWI (full waveform inversion) code which simultaneously runs on the CPUs and on the co-processors installed in a workstation. The main advantage of running a 2D FWI on a workstation is to be able to quickly evaluate new features such as more complicated wave equations, new cost functions, finite-difference stencils or boundary conditions. Since the co-processor is made of 61 in-order x86 cores, each of them having up to 4 threads, this many-core can be seen as a shared memory SMP (symmetric multiprocessing) machine with its own IP address. Depending on the vendor, a single workstation can handle several co-processors making the workstation as a personal cluster under the desk. The original Fortran 90 CPU version of the 2D FWI code is just recompiled to get a Xeon Phi x86 binary. This multi and many-core configuration uses standard compilers and associated MPI as well as math libraries under Linux; therefore, the cost of code development remains constant, while improving computation time. We choose to implement the code with the so-called symmetric mode to fully use the capacity of the workstation, but we also evaluate the scalability of the code in native mode (i.e running only on the co-processor) thanks to the Linux ssh and NFS capabilities. Usual care of optimization and SIMD vectorization is used to ensure optimal performances, and to analyze the application performances and bottlenecks on both platforms. The 2D FWI implementation uses finite-difference time-domain forward modeling and a quasi-Newton (with L-BFGS algorithm) optimization scheme for the model parameters update. Parallelization is achieved through standard MPI shot gathers distribution and OpenMP for domain decomposition within the co-processor. Taking advantage of the 16 GB of memory available on the co-processor we are able to keep wavefields in memory to achieve the gradient computation by cross-correlation of forward and back-propagated wavefields needed by our time-domain FWI scheme, without heavy traffic on the i/o subsystem and PCIe bus. In this presentation we will also review some simple methodologies to determine performance expectation compared to real performances in order to get optimization effort estimation before starting any huge modification or rewriting of research codes. The key message is the ease of use and development of this hybrid configuration to reach not the absolute peak performance value but the optimal one that ensures the best balance between geophysical and computer developments.

Fast in-memory elastic full-waveform inversion using consumer-grade GPUs

NASA Astrophysics Data System (ADS)

Sivertsen Bergslid, Tore; Birger Raknes, Espen; Arntsen, Børge

2017-04-01

Full-waveform inversion (FWI) is a technique to estimate subsurface properties by using the recorded waveform produced by a seismic source and applying inverse theory. This is done through an iterative optimization procedure, where each iteration requires solving the wave equation many times, then trying to minimize the difference between the modeled and the measured seismic data. Having to model many of these seismic sources per iteration means that this is a highly computationally demanding procedure, which usually involves writing a lot of data to disk. We have written code that does forward modeling and inversion entirely in memory. A typical HPC cluster has many more CPUs than GPUs. Since FWI involves modeling many seismic sources per iteration, the obvious approach is to parallelize the code on a source-by-source basis, where each core of the CPU performs one modeling, and do all modelings simultaneously. With this approach, the GPU is already at a major disadvantage in pure numbers. Fortunately, GPUs can more than make up for this hardware disadvantage by performing each modeling much faster than a CPU. Another benefit of parallelizing each individual modeling is that it lets each modeling use a lot more RAM. If one node has 128 GB of RAM and 20 CPU cores, each modeling can use only 6.4 GB RAM if one is running the node at full capacity with source-by-source parallelization on the CPU. A parallelized per-source code using GPUs can use 64 GB RAM per modeling. Whenever a modeling uses more RAM than is available and has to start using regular disk space the runtime increases dramatically, due to slow file I/O. The extremely high computational speed of the GPUs combined with the large amount of RAM available for each modeling lets us do high frequency FWI for fairly large models very quickly. For a single modeling, our GPU code outperforms the single-threaded CPU-code by a factor of about 75. Successful inversions have been run on data with frequencies up to 40 Hz for a model of 2001 by 600 grid points with 5 m grid spacing and 5000 time steps, in less than 2.5 minutes per source. In practice, using 15 nodes (30 GPUs) to model 101 sources, each iteration took approximately 9 minutes. For reference, the same inversion run with our CPU code uses two hours per iteration. This was done using only a very simple wavefield interpolation technique, saving every second timestep. Using a more sophisticated checkpointing or wavefield reconstruction method would allow us to increase this model size significantly. Our results show that ordinary gaming GPUs are a viable alternative to the expensive professional GPUs often used today, when performing large scale modeling and inversion in geophysics.

A Very Fast and Angular Momentum Conserving Tree Code

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

Marcello, Dominic C., E-mail: dmarce504@gmail.com

There are many methods used to compute the classical gravitational field in astrophysical simulation codes. With the exception of the typically impractical method of direct computation, none ensure conservation of angular momentum to machine precision. Under uniform time-stepping, the Cartesian fast multipole method of Dehnen (also known as the very fast tree code) conserves linear momentum to machine precision. We show that it is possible to modify this method in a way that conserves both angular and linear momenta.

CMacIonize: Monte Carlo photoionisation and moving-mesh radiation hydrodynamics

NASA Astrophysics Data System (ADS)

Vandenbroucke, Bert; Wood, Kenneth

2018-02-01

CMacIonize simulates the self-consistent evolution of HII regions surrounding young O and B stars, or other sources of ionizing radiation. The code combines a Monte Carlo photoionization algorithm that uses a complex mix of hydrogen, helium and several coolants in order to self-consistently solve for the ionization and temperature balance at any given time, with a standard first order hydrodynamics scheme. The code can be run as a post-processing tool to get the line emission from an existing simulation snapshot, but can also be used to run full radiation hydrodynamical simulations. Both the radiation transfer and the hydrodynamics are implemented in a general way that is independent of the grid structure that is used to discretize the system, allowing it to be run both as a standard fixed grid code and also as a moving-mesh code.

Generation of signature databases with fast codes

NASA Astrophysics Data System (ADS)

Bradford, Robert A.; Woodling, Arthur E.; Brazzell, James S.

1990-09-01

Using the FASTSIG signature code to generate optical signature databases for the Ground-based Surveillance and Traking System (GSTS) Program has improved the efficiency of the database generation process. The goal of the current GSTS database is to provide standardized, threat representative target signatures that can easily be used for acquisition and trk studies, discrimination algorithm development, and system simulations. Large databases, with as many as eight interpolalion parameters, are required to maintain the fidelity demands of discrimination and to generalize their application to other strateg systems. As the need increases for quick availability of long wave infrared (LWIR) target signatures for an evolving design4o-threat, FASTSIG has become a database generation alternative to using the industry standard OptiCal Signatures Code (OSC). FASTSIG, developed in 1985 to meet the unique strategic systems demands imposed by the discrimination function, has the significant advantage of being a faster running signature code than the OSC, typically requiring two percent of the cpu time. It uses analytical approximations to model axisymmetric targets, with the fidelity required for discrimination analysis. Access of the signature database is accomplished through use of the waveband integration and interpolation software, INTEG and SIGNAT. This paper gives details of this procedure as well as sample interpolated signatures and also covers sample verification by comparison to the OSC, in order to establish the fidelity of the FASTSIG generated database.

SPIDERMAN: an open-source code to model phase curves and secondary eclipses

NASA Astrophysics Data System (ADS)

Louden, Tom; Kreidberg, Laura

2018-06-01

We present SPIDERMAN (Secondary eclipse and Phase curve Integrator for 2D tempERature MAppiNg), a fast code for calculating exoplanet phase curves and secondary eclipses with arbitrary surface brightness distributions in two dimensions. Using a geometrical algorithm, the code solves exactly the area of sections of the disc of the planet that are occulted by the star. The code is written in C with a user-friendly Python interface, and is optimized to run quickly, with no loss in numerical precision. Approximately 1000 models can be generated per second in typical use, making Markov Chain Monte Carlo analyses practicable. The modular nature of the code allows easy comparison of the effect of multiple different brightness distributions for the data set. As a test case, we apply the code to archival data on the phase curve of WASP-43b using a physically motivated analytical model for the two-dimensional brightness map. The model provides a good fit to the data; however, it overpredicts the temperature of the nightside. We speculate that this could be due to the presence of clouds on the nightside of the planet, or additional reflected light from the dayside. When testing a simple cloud model, we find that the best-fitting model has a geometric albedo of 0.32 ± 0.02 and does not require a hot nightside. We also test for variation of the map parameters as a function of wavelength and find no statistically significant correlations. SPIDERMAN is available for download at https://github.com/tomlouden/spiderman.

Aeroelastic Tailoring Study of N+2 Low-Boom Supersonic Commercial Transport Aircraft

NASA Technical Reports Server (NTRS)

Pak, Chan-gi

2015-01-01

The Lockheed Martins N+2 Low-boom Supersonic Commercial Transport (LSCT) aircraft is optimized in this study through the use of a multidisciplinary design optimization tool developed at the NASA Armstrong Flight Research Center. A total of 111 design variables are used in the first optimization run. Total structural weight is the objective function in this optimization run. Design requirements for strength, buckling, and flutter are selected as constraint functions during the first optimization run. The MSC Nastran code is used to obtain the modal, strength, and buckling characteristics. Flutter and trim analyses are based on ZAERO code and landing and ground control loads are computed using an in-house code.

Initial results from the NSTX Real-Time Velocity diagnostic

NASA Astrophysics Data System (ADS)

Podesta, M.; Bell, R. E.

2011-10-01

A new diagnostic for fast measurements of plasma rotation through active charge-exchange recombination spectroscopy (CHERS) was installed on NSTX. The diagnostic infers toroidal rotation from carbon ions undergoing charge-exchange with neutrals from a heating Neutral Beam (NB). Each of the 4 channels, distributed along the outer major radius, includes active views intercepting the NB and background views missing the beam. Estimated uncertainties in the measured velocity are <5% at the maximum sampling rate of 5000 Hz (or <1% at 1000 Hz), to be compared with <0.5% and 100 Hz of the main NSTX CHERS system. Signals are acquired on 2 CCD detectors, each controlled by a dedicated PC. Spectra are fitted in real-time through a C++ processing code and velocities are made available to the Plasma Control System for future implementation of feedback on velocity. Results from the initial operation during the 2011 run are discussed, emphasizing the fast dynamics of toroidal rotation, e . g . during L-H mode transition and breaking caused by instabilities and by externally-imposed magnetic perturbations. Work supported by USDOE Contract No. DE-AC02-09CH11466.

Validation of fast-ion D-alpha spectrum measurements during EAST neutral-beam heated plasmas

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

Huang, J., E-mail: juan.huang@ipp.ac.cn; Wu, C. R.; Hou, Y. M.

2016-11-15

To investigate the fast ion behavior, a fast ion D-alpha (FIDA) diagnostic system has been installed on EAST. Fast ion features can be inferred from the Doppler shifted spectrum of Balmer-alpha light from energetic hydrogenic atoms. This paper will focus on the validation of FIDA measurements performed using MHD-quiescent discharges in 2015 campaign. Two codes have been applied to calculate the D{sub α} spectrum: one is a Monte Carlo code, Fortran 90 version FIDASIM, and the other is an analytical code, Simulation of Spectra (SOS). The predicted SOS fast-ion spectrum agrees well with the measurement; however, the level of fast-ionmore » part from FIDASIM is lower. The discrepancy is possibly due to the difference between FIDASIM and SOS velocity distribution function. The details will be presented in the paper to primarily address comparisons of predicted and observed spectrum shapes/amplitudes.« less

Aeroelastic Tailoring Study of N+2 Low Boom Supersonic Commerical Transport Aircraft

NASA Technical Reports Server (NTRS)

Pak, Chan-Gi

2015-01-01

The Lockheed Martin N+2 Low - boom Supersonic Commercial Transport (LSCT) aircraft was optimized in this study through the use of a multidisciplinary design optimization tool developed at the National Aeronautics and S pace Administration Armstrong Flight Research Center. A total of 111 design variables we re used in the first optimization run. Total structural weight was the objective function in this optimization run. Design requirements for strength, buckling, and flutter we re selected as constraint functions during the first optimization run. The MSC Nastran code was used to obtain the modal, strength, and buckling characteristics. Flutter and trim analyses we re based on ZAERO code, and landing and ground control loads were computed using an in - house code. The w eight penalty to satisfy all the design requirement s during the first optimization run was 31,367 lb, a 9.4% increase from the baseline configuration. The second optimization run was prepared and based on the big-bang big-crunch algorithm. Six composite ply angles for the second and fourth composite layers were selected as discrete design variables for the second optimization run. Composite ply angle changes can't improve the weight configuration of the N+2 LSCT aircraft. However, this second optimization run can create more tolerance for the active and near active strength constraint values for future weight optimization runs.

Leadership Class Configuration Interaction Code - Status and Opportunities

NASA Astrophysics Data System (ADS)

Vary, James

2011-10-01

With support from SciDAC-UNEDF (www.unedf.org) nuclear theorists have developed and are continuously improving a Leadership Class Configuration Interaction Code (LCCI) for forefront nuclear structure calculations. The aim of this project is to make state-of-the-art nuclear structure tools available to the entire community of researchers including graduate students. The project includes codes such as NuShellX, MFDn and BIGSTICK that run a range of computers from laptops to leadership class supercomputers. Codes, scripts, test cases and documentation have been assembled, are under continuous development and are scheduled for release to the entire research community in November 2011. A covering script that accesses the appropriate code and supporting files is under development. In addition, a Data Base Management System (DBMS) that records key information from large production runs and archived results of those runs has been developed (http://nuclear.physics.iastate.edu/info/) and will be released. Following an outline of the project, the code structure, capabilities, the DBMS and current efforts, I will suggest a path forward that would benefit greatly from a significant partnership between researchers who use the codes, code developers and the National Nuclear Data efforts. This research is supported in part by DOE under grant DE-FG02-87ER40371 and grant DE-FC02-09ER41582 (SciDAC-UNEDF).

Self-Scheduling Parallel Methods for Multiple Serial Codes with Application to WOPWOP

NASA Technical Reports Server (NTRS)

Long, Lyle N.; Brentner, Kenneth S.

2000-01-01

This paper presents a scheme for efficiently running a large number of serial jobs on parallel computers. Two examples are given of computer programs that run relatively quickly, but often they must be run numerous times to obtain all the results needed. It is very common in science and engineering to have codes that are not massive computing challenges in themselves, but due to the number of instances that must be run, they do become large-scale computing problems. The two examples given here represent common problems in aerospace engineering: aerodynamic panel methods and aeroacoustic integral methods. The first example simply solves many systems of linear equations. This is representative of an aerodynamic panel code where someone would like to solve for numerous angles of attack. The complete code for this first example is included in the appendix so that it can be readily used by others as a template. The second example is an aeroacoustics code (WOPWOP) that solves the Ffowcs Williams Hawkings equation to predict the far-field sound due to rotating blades. In this example, one quite often needs to compute the sound at numerous observer locations, hence parallelization is utilized to automate the noise computation for a large number of observers.

Visual saliency-based fast intracoding algorithm for high efficiency video coding

NASA Astrophysics Data System (ADS)

Zhou, Xin; Shi, Guangming; Zhou, Wei; Duan, Zhemin

2017-01-01

Intraprediction has been significantly improved in high efficiency video coding over H.264/AVC with quad-tree-based coding unit (CU) structure from size 64×64 to 8×8 and more prediction modes. However, these techniques cause a dramatic increase in computational complexity. An intracoding algorithm is proposed that consists of perceptual fast CU size decision algorithm and fast intraprediction mode decision algorithm. First, based on the visual saliency detection, an adaptive and fast CU size decision method is proposed to alleviate intraencoding complexity. Furthermore, a fast intraprediction mode decision algorithm with step halving rough mode decision method and early modes pruning algorithm is presented to selectively check the potential modes and effectively reduce the complexity of computation. Experimental results show that our proposed fast method reduces the computational complexity of the current HM to about 57% in encoding time with only 0.37% increases in BD rate. Meanwhile, the proposed fast algorithm has reasonable peak signal-to-noise ratio losses and nearly the same subjective perceptual quality.

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.

Assessing the Role of Place and Timing Cues in Coding Frequency and Amplitude Modulation as a Function of Age.

PubMed

Whiteford, Kelly L; Kreft, Heather A; Oxenham, Andrew J

2017-08-01

Natural sounds can be characterized by their fluctuations in amplitude and frequency. Ageing may affect sensitivity to some forms of fluctuations more than others. The present study used individual differences across a wide age range (20-79 years) to test the hypothesis that slow-rate, low-carrier frequency modulation (FM) is coded by phase-locked auditory-nerve responses to temporal fine structure (TFS), whereas fast-rate FM is coded via rate-place (tonotopic) cues, based on amplitude modulation (AM) of the temporal envelope after cochlear filtering. Using a low (500 Hz) carrier frequency, diotic FM and AM detection thresholds were measured at slow (1 Hz) and fast (20 Hz) rates in 85 listeners. Frequency selectivity and TFS coding were assessed using forward masking patterns and interaural phase disparity tasks (slow dichotic FM), respectively. Comparable interaural level disparity tasks (slow and fast dichotic AM and fast dichotic FM) were measured to control for effects of binaural processing not specifically related to TFS coding. Thresholds in FM and AM tasks were correlated, even across tasks thought to use separate peripheral codes. Age was correlated with slow and fast FM thresholds in both diotic and dichotic conditions. The relationship between age and AM thresholds was generally not significant. Once accounting for AM sensitivity, only diotic slow-rate FM thresholds remained significantly correlated with age. Overall, results indicate stronger effects of age on FM than AM. However, because of similar effects for both slow and fast FM when not accounting for AM sensitivity, the effects cannot be unambiguously ascribed to TFS coding.

[Ironman Triathlon].

PubMed

Knechtle, Beat; Nikolaidis, Pantelis T; Rosemann, Thomas; Rüst, Christoph A

2016-06-22

Every year, thousands of triathletes try to qualify for the «Ironman Hawaii» (3,8 km swimming, 180 km cycling and 42,195 km running), the World Championship of long-distance triathletes. In this overview, we present the recent findings in literature with the most important variables with an influence on Ironman triathlon performance. The most important performance-influencing factors for a fast Ironman race time for both women and men are a large training volume and a high intensity in training, a large volume being more important than a high intensity, a low percentage of body fat, an ideal age of 30–35 years, a fast personal best in the Olympic distance triathlon (1,5 km swimming, 40 km cycling and 10 km running), a fast personal best in marathon running and origin from the United States of America.

Statistical Analysis of CFD Solutions from 2nd Drag Prediction Workshop

NASA Technical Reports Server (NTRS)

Hemsch, M. J.; Morrison, J. H.

2004-01-01

In June 2001, the first AIAA Drag Prediction Workshop was held to evaluate results obtained from extensive N-Version testing of a series of RANS CFD codes. The geometry used for the computations was the DLR-F4 wing-body combination which resembles a medium-range subsonic transport. The cases reported include the design cruise point, drag polars at eight Mach numbers, and drag rise at three values of lift. Although comparisons of the code-to-code medians with available experimental data were similar to those obtained in previous studies, the code-to-code scatter was more than an order-of-magnitude larger than expected and far larger than desired for design and for experimental validation. The second Drag Prediction Workshop was held in June 2003 with emphasis on the determination of installed pylon-nacelle drag increments and on grid refinement studies. The geometry used was the DLR-F6 wing-body-pylon-nacelle combination for which the design cruise point and the cases run were similar to the first workshop except for additional runs on coarse and fine grids to complement the runs on medium grids. The code-to-code scatter was significantly reduced for the wing-body configuration compared to the first workshop, although still much larger than desired. However, the grid refinement studies showed no sign$cant improvement in code-to-code scatter with increasing grid refinement.

PconsD: ultra rapid, accurate model quality assessment for protein structure prediction.

PubMed

Skwark, Marcin J; Elofsson, Arne

2013-07-15

Clustering methods are often needed for accurately assessing the quality of modeled protein structures. Recent blind evaluation of quality assessment methods in CASP10 showed that there is little difference between many different methods as far as ranking models and selecting best model are concerned. When comparing many models, the computational cost of the model comparison can become significant. Here, we present PconsD, a fast, stream-computing method for distance-driven model quality assessment that runs on consumer hardware. PconsD is at least one order of magnitude faster than other methods of comparable accuracy. The source code for PconsD is freely available at http://d.pcons.net/. Supplementary benchmarking data are also available there. arne@bioinfo.se Supplementary data are available at Bioinformatics online.

Capturing atmospheric effects on 3D millimeter wave radar propagation patterns

NASA Astrophysics Data System (ADS)

Cook, Richard D.; Fiorino, Steven T.; Keefer, Kevin J.; Stringer, Jeremy

2016-05-01

Traditional radar propagation modeling is done using a path transmittance with little to no input for weather and atmospheric conditions. As radar advances into the millimeter wave (MMW) regime, atmospheric effects such as attenuation and refraction become more pronounced than at traditional radar wavelengths. The DoD High Energy Laser Joint Technology Offices High Energy Laser End-to-End Operational Simulation (HELEEOS) in combination with the Laser Environmental Effects Definition and Reference (LEEDR) code have shown great promise simulating atmospheric effects on laser propagation. Indeed, the LEEDR radiative transfer code has been validated in the UV through RF. Our research attempts to apply these models to characterize the far field radar pattern in three dimensions as a signal propagates from an antenna towards a point in space. Furthermore, we do so using realistic three dimensional atmospheric profiles. The results from these simulations are compared to those from traditional radar propagation software packages. In summary, a fast running method has been investigated which can be incorporated into computational models to enhance understanding and prediction of MMW propagation through various atmospheric and weather conditions.

Second order gyrokinetic theory for particle-in-cell codes

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

Tronko, Natalia; Bottino, Alberto; Sonnendrücker, Eric

2016-08-15

The main idea of the gyrokinetic dynamical reduction consists in a systematical removal of the fast scale motion (the gyromotion) from the dynamics of the plasma, resulting in a considerable simplification and a significant gain of computational time. The gyrokinetic Maxwell–Vlasov equations are nowadays implemented in for modeling (both laboratory and astrophysical) strongly magnetized plasmas. Different versions of the reduced set of equations exist, depending on the construction of the gyrokinetic reduction procedure and the approximations performed in the derivation. The purpose of this article is to explicitly show the connection between the general second order gyrokinetic Maxwell–Vlasov system issuedmore » from the modern gyrokinetic theory and the model currently implemented in the global electromagnetic Particle-in-Cell code ORB5. Necessary information about the modern gyrokinetic formalism is given together with the consistent derivation of the gyrokinetic Maxwell–Vlasov equations from first principles. The variational formulation of the dynamics is used to obtain the corresponding energy conservation law, which in turn is used for the verification of energy conservation diagnostics currently implemented in ORB5. This work fits within the context of the code verification project VeriGyro currently run at IPP Max-Planck Institut in collaboration with others European institutions.« less

Rcount: simple and flexible RNA-Seq read counting.

PubMed

Schmid, Marc W; Grossniklaus, Ueli

2015-02-01

Analysis of differential gene expression by RNA sequencing (RNA-Seq) is frequently done using feature counts, i.e. the number of reads mapping to a gene. However, commonly used count algorithms (e.g. HTSeq) do not address the problem of reads aligning with multiple locations in the genome (multireads) or reads aligning with positions where two or more genes overlap (ambiguous reads). Rcount specifically addresses these issues. Furthermore, Rcount allows the user to assign priorities to certain feature types (e.g. higher priority for protein-coding genes compared to rRNA-coding genes) or to add flanking regions. Rcount provides a fast and easy-to-use graphical user interface requiring no command line or programming skills. It is implemented in C++ using the SeqAn (www.seqan.de) and the Qt libraries (qt-project.org). Source code and 64 bit binaries for (Ubuntu) Linux, Windows (7) and MacOSX are released under the GPLv3 license and are freely available on github.com/MWSchmid/Rcount. marcschmid@gmx.ch Test data, genome annotation files, useful Python and R scripts and a step-by-step user guide (including run-time and memory usage tests) are available on github.com/MWSchmid/Rcount. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Ion absorption of the high harmonic fast wave in the National Spherical Torus Experiment

NASA Astrophysics Data System (ADS)

Rosenberg, Adam Lewis

Ion absorption of the high harmonic fast wave in a spherical torus is of critical importance to assessing the viability of the wave as a means of heating and driving current. Analysis of recent NSTX shots has revealed that under some conditions when neutral beam and RF power are injected into the plasma simultaneously, a fast ion population with energy above the beam injection energy is sustained by the wave. In agreement with modeling, these experiments find the RF-induced fast ion tail strength and neutron rate at lower B-fields to be less enhanced, likely due to a larger β profile, which promotes greater off-axis absorption where the fast ion population is small. Ion loss codes find the increased loss fraction with decreased B insufficient to account for the changes in tail strength, providing further evidence that this is an RF interaction effect. Though greater ion absorption is predicted with lower k∥, surprisingly little variation in the tail was observed, along with a neutron rate enhancement with higher k∥. Data from the neutral particle analyzer, neutron detectors, x-ray crystal spectrometer, and Thomson scattering is presented, along with results from the TRANSP transport analysis code, ray-tracing codes HPRT and CURRAY, full-wave code and AORSA, quasilinear code CQL3D, and ion loss codes EIGOL and CONBEAM.

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.

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.

libRoadRunner: a high performance SBML simulation and analysis library

PubMed Central

Somogyi, Endre T.; Bouteiller, Jean-Marie; Glazier, James A.; König, Matthias; Medley, J. Kyle; Swat, Maciej H.; Sauro, Herbert M.

2015-01-01

Motivation: This article presents libRoadRunner, an extensible, high-performance, cross-platform, open-source software library for the simulation and analysis of models expressed using Systems Biology Markup Language (SBML). SBML is the most widely used standard for representing dynamic networks, especially biochemical networks. libRoadRunner is fast enough to support large-scale problems such as tissue models, studies that require large numbers of repeated runs and interactive simulations. Results: libRoadRunner is a self-contained library, able to run both as a component inside other tools via its C++ and C bindings, and interactively through its Python interface. Its Python Application Programming Interface (API) is similar to the APIs of MATLAB (www.mathworks.com) and SciPy (http://www.scipy.org/), making it fast and easy to learn. libRoadRunner uses a custom Just-In-Time (JIT) compiler built on the widely used LLVM JIT compiler framework. It compiles SBML-specified models directly into native machine code for a variety of processors, making it appropriate for solving extremely large models or repeated runs. libRoadRunner is flexible, supporting the bulk of the SBML specification (except for delay and non-linear algebraic equations) including several SBML extensions (composition and distributions). It offers multiple deterministic and stochastic integrators, as well as tools for steady-state analysis, stability analysis and structural analysis of the stoichiometric matrix. Availability and implementation: libRoadRunner binary distributions are available for Mac OS X, Linux and Windows. The library is licensed under Apache License Version 2.0. libRoadRunner is also available for ARM-based computers such as the Raspberry Pi. http://www.libroadrunner.org provides online documentation, full build instructions, binaries and a git source repository. Contacts: hsauro@u.washington.edu or somogyie@indiana.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26085503

libRoadRunner: a high performance SBML simulation and analysis library.

PubMed

Somogyi, Endre T; Bouteiller, Jean-Marie; Glazier, James A; König, Matthias; Medley, J Kyle; Swat, Maciej H; Sauro, Herbert M

2015-10-15

This article presents libRoadRunner, an extensible, high-performance, cross-platform, open-source software library for the simulation and analysis of models expressed using Systems Biology Markup Language (SBML). SBML is the most widely used standard for representing dynamic networks, especially biochemical networks. libRoadRunner is fast enough to support large-scale problems such as tissue models, studies that require large numbers of repeated runs and interactive simulations. libRoadRunner is a self-contained library, able to run both as a component inside other tools via its C++ and C bindings, and interactively through its Python interface. Its Python Application Programming Interface (API) is similar to the APIs of MATLAB ( WWWMATHWORKSCOM: ) and SciPy ( HTTP//WWWSCIPYORG/: ), making it fast and easy to learn. libRoadRunner uses a custom Just-In-Time (JIT) compiler built on the widely used LLVM JIT compiler framework. It compiles SBML-specified models directly into native machine code for a variety of processors, making it appropriate for solving extremely large models or repeated runs. libRoadRunner is flexible, supporting the bulk of the SBML specification (except for delay and non-linear algebraic equations) including several SBML extensions (composition and distributions). It offers multiple deterministic and stochastic integrators, as well as tools for steady-state analysis, stability analysis and structural analysis of the stoichiometric matrix. libRoadRunner binary distributions are available for Mac OS X, Linux and Windows. The library is licensed under Apache License Version 2.0. libRoadRunner is also available for ARM-based computers such as the Raspberry Pi. http://www.libroadrunner.org provides online documentation, full build instructions, binaries and a git source repository. hsauro@u.washington.edu or somogyie@indiana.edu Supplementary data are available at Bioinformatics online. Published by Oxford University Press 2015. This work is written by US Government employees and is in the public domain in the US.

Grid Oriented Implementation of the Tephra Model

NASA Astrophysics Data System (ADS)

Coltelli, M.; D'Agostino, M.; Drago, A.; Pistagna, F.; Prestifilippo, M.; Reitano, D.; Scollo, S.; Spata, G.

2009-04-01

TEPHRA is a two dimensional advection-diffusion model implemented by Bonadonna et al. [2005] that describes the sedimentation process of particles from volcanic plumes. The model is used by INGV - Istituto Nazionale di Geofisica e Vulcanologia, Sezione di Catania, to forecast tephra dispersion during Etna volcanic events. Every day weather forecast provided by the Italian Air Force Meteorological Office in Rome and by the hydrometeorological service of ARPA in Emilia Romagna are processed by TEPHRA model with other volcanological parameters to simulate two different eruptive scenarios of Mt. Etna (corresponding to 1998 and 2002-03 Etna eruptions). The model outputs are plotted on maps and transferred to Civil Protection which takes the trouble to give public warnings and plan mitigation measures. The TEPHRA model is implemented in ANSI-C code using MPI commands to maximize parallel computation. Actually the model runs on an INGV Beowulf cluster. In order to provide better performances we worked on porting it to PI2S2 sicilian grid infrastructure inside the "PI2S2 Project" (2006-2008). We configured the application to run on grid, using Glite middleware, analyzed the obtained performances and comparing them with ones obtained on the local cluster. As TEPHRA needs to be run in a short time in order to transfer fastly the dispersion maps to Civil Protection, we also worked to minimize and stabilize grid job-scheduling time by using customized high-priority queues called Emergency Queue.

Development of a GPU Compatible Version of the Fast Radiation Code RRTMG

NASA Astrophysics Data System (ADS)

Iacono, M. J.; Mlawer, E. J.; Berthiaume, D.; Cady-Pereira, K. E.; Suarez, M.; Oreopoulos, L.; Lee, D.

2012-12-01

The absorption of solar radiation and emission/absorption of thermal radiation are crucial components of the physics that drive Earth's climate and weather. Therefore, accurate radiative transfer calculations are necessary for realistic climate and weather simulations. Efficient radiation codes have been developed for this purpose, but their accuracy requirements still necessitate that as much as 30% of the computational time of a GCM is spent computing radiative fluxes and heating rates. The overall computational expense constitutes a limitation on a GCM's predictive ability if it becomes an impediment to adding new physics to or increasing the spatial and/or vertical resolution of the model. The emergence of Graphics Processing Unit (GPU) technology, which will allow the parallel computation of multiple independent radiative calculations in a GCM, will lead to a fundamental change in the competition between accuracy and speed. Processing time previously consumed by radiative transfer will now be available for the modeling of other processes, such as physics parameterizations, without any sacrifice in the accuracy of the radiative transfer. Furthermore, fast radiation calculations can be performed much more frequently and will allow the modeling of radiative effects of rapid changes in the atmosphere. The fast radiation code RRTMG, developed at Atmospheric and Environmental Research (AER), is utilized operationally in many dynamical models throughout the world. We will present the results from the first stage of an effort to create a version of the RRTMG radiation code designed to run efficiently in a GPU environment. This effort will focus on the RRTMG implementation in GEOS-5. RRTMG has an internal pseudo-spectral vector of length of order 100 that, when combined with the much greater length of the global horizontal grid vector from which the radiation code is called in GEOS-5, makes RRTMG/GEOS-5 particularly suited to achieving a significant speed improvement through GPU technology. This large number of independent cases will allow us to take full advantage of the computational power of the latest GPUs, ensuring that all thread cores in the GPU remain active, a key criterion for obtaining significant speedup. The CUDA (Compute Unified Device Architecture) Fortran compiler developed by PGI and Nvidia will allow us to construct this parallel implementation on the GPU while remaining in the Fortran language. This implementation will scale very well across various CUDA-supported GPUs such as the recently released Fermi Nvidia cards. We will present the computational speed improvements of the GPU-compatible code relative to the standard CPU-based RRTMG with respect to a very large and diverse suite of atmospheric profiles. This suite will also be utilized to demonstrate the minimal impact of the code restructuring on the accuracy of radiation calculations. The GPU-compatible version of RRTMG will be directly applicable to future versions of GEOS-5, but it is also likely to provide significant associated benefits for other GCMs that employ RRTMG.

VAC: Versatile Advection Code

NASA Astrophysics Data System (ADS)

Tóth, Gábor; Keppens, Rony

2012-07-01

The Versatile Advection Code (VAC) is a freely available general hydrodynamic and magnetohydrodynamic simulation software that works in 1, 2 or 3 dimensions on Cartesian and logically Cartesian grids. VAC runs on any Unix/Linux system with a Fortran 90 (or 77) compiler and Perl interpreter. VAC can run on parallel machines using either the Message Passing Interface (MPI) library or a High Performance Fortran (HPF) compiler.

NEQAIR96,Nonequilibrium and Equilibrium Radiative Transport and Spectra Program: User's Manual

NASA Technical Reports Server (NTRS)

Whiting, Ellis E.; Park, Chul; Liu, Yen; Arnold, James O.; Paterson, John A.

1996-01-01

This document is the User's Manual for a new version of the NEQAIR computer program, NEQAIR96. The program is a line-by-line and a line-of-sight code. It calculates the emission and absorption spectra for atomic and diatomic molecules and the transport of radiation through a nonuniform gas mixture to a surface. The program has been rewritten to make it easy to use, run faster, and include many run-time options that tailor a calculation to the user's requirements. The accuracy and capability have also been improved by including the rotational Hamiltonian matrix formalism for calculating rotational energy levels and Hoenl-London factors for dipole and spin-allowed singlet, doublet, triplet, and quartet transitions. Three sample cases are also included to help the user become familiar with the steps taken to produce a spectrum. A new user interface is included that uses check location, to select run-time options and to enter selected run data, making NEQAIR96 easier to use than the older versions of the code. The ease of its use and the speed of its algorithms make NEQAIR96 a valuable educational code as well as a practical spectroscopic prediction and diagnostic code.

High-Throughput Computation and the Applicability of Monte Carlo Integration in Fatigue Load Estimation of Floating Offshore Wind Turbines

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

Graf, Peter A.; Stewart, Gordon; Lackner, Matthew

Long-term fatigue loads for floating offshore wind turbines are hard to estimate because they require the evaluation of the integral of a highly nonlinear function over a wide variety of wind and wave conditions. Current design standards involve scanning over a uniform rectangular grid of metocean inputs (e.g., wind speed and direction and wave height and period), which becomes intractable in high dimensions as the number of required evaluations grows exponentially with dimension. Monte Carlo integration offers a potentially efficient alternative because it has theoretical convergence proportional to the inverse of the square root of the number of samples, whichmore » is independent of dimension. In this paper, we first report on the integration of the aeroelastic code FAST into NREL's systems engineering tool, WISDEM, and the development of a high-throughput pipeline capable of sampling from arbitrary distributions, running FAST on a large scale, and postprocessing the results into estimates of fatigue loads. Second, we use this tool to run a variety of studies aimed at comparing grid-based and Monte Carlo-based approaches with calculating long-term fatigue loads. We observe that for more than a few dimensions, the Monte Carlo approach can represent a large improvement in computational efficiency, but that as nonlinearity increases, the effectiveness of Monte Carlo is correspondingly reduced. The present work sets the stage for future research focusing on using advanced statistical methods for analysis of wind turbine fatigue as well as extreme loads.« less

Fast analysis of molecular dynamics trajectories with graphics processing units-Radial distribution function histogramming

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

Levine, Benjamin G., E-mail: ben.levine@temple.ed; Stone, John E., E-mail: johns@ks.uiuc.ed; Kohlmeyer, Axel, E-mail: akohlmey@temple.ed

2011-05-01

The calculation of radial distribution functions (RDFs) from molecular dynamics trajectory data is a common and computationally expensive analysis task. The rate limiting step in the calculation of the RDF is building a histogram of the distance between atom pairs in each trajectory frame. Here we present an implementation of this histogramming scheme for multiple graphics processing units (GPUs). The algorithm features a tiling scheme to maximize the reuse of data at the fastest levels of the GPU's memory hierarchy and dynamic load balancing to allow high performance on heterogeneous configurations of GPUs. Several versions of the RDF algorithm aremore » presented, utilizing the specific hardware features found on different generations of GPUs. We take advantage of larger shared memory and atomic memory operations available on state-of-the-art GPUs to accelerate the code significantly. The use of atomic memory operations allows the fast, limited-capacity on-chip memory to be used much more efficiently, resulting in a fivefold increase in performance compared to the version of the algorithm without atomic operations. The ultimate version of the algorithm running in parallel on four NVIDIA GeForce GTX 480 (Fermi) GPUs was found to be 92 times faster than a multithreaded implementation running on an Intel Xeon 5550 CPU. On this multi-GPU hardware, the RDF between two selections of 1,000,000 atoms each can be calculated in 26.9 s per frame. The multi-GPU RDF algorithms described here are implemented in VMD, a widely used and freely available software package for molecular dynamics visualization and analysis.« less

Fast Analysis of Molecular Dynamics Trajectories with Graphics Processing Units—Radial Distribution Function Histogramming

PubMed Central

Stone, John E.; Kohlmeyer, Axel

2011-01-01

The calculation of radial distribution functions (RDFs) from molecular dynamics trajectory data is a common and computationally expensive analysis task. The rate limiting step in the calculation of the RDF is building a histogram of the distance between atom pairs in each trajectory frame. Here we present an implementation of this histogramming scheme for multiple graphics processing units (GPUs). The algorithm features a tiling scheme to maximize the reuse of data at the fastest levels of the GPU’s memory hierarchy and dynamic load balancing to allow high performance on heterogeneous configurations of GPUs. Several versions of the RDF algorithm are presented, utilizing the specific hardware features found on different generations of GPUs. We take advantage of larger shared memory and atomic memory operations available on state-of-the-art GPUs to accelerate the code significantly. The use of atomic memory operations allows the fast, limited-capacity on-chip memory to be used much more efficiently, resulting in a fivefold increase in performance compared to the version of the algorithm without atomic operations. The ultimate version of the algorithm running in parallel on four NVIDIA GeForce GTX 480 (Fermi) GPUs was found to be 92 times faster than a multithreaded implementation running on an Intel Xeon 5550 CPU. On this multi-GPU hardware, the RDF between two selections of 1,000,000 atoms each can be calculated in 26.9 seconds per frame. The multi-GPU RDF algorithms described here are implemented in VMD, a widely used and freely available software package for molecular dynamics visualization and analysis. PMID:21547007

Review of Hybrid (Deterministic/Monte Carlo) Radiation Transport Methods, Codes, and Applications at Oak Ridge National Laboratory

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

Wagner, John C; Peplow, Douglas E.; Mosher, Scott W

2011-01-01

This paper provides a review of the hybrid (Monte Carlo/deterministic) radiation transport methods and codes used at the Oak Ridge National Laboratory and examples of their application for increasing the efficiency of real-world, fixed-source Monte Carlo analyses. The two principal hybrid methods are (1) Consistent Adjoint Driven Importance Sampling (CADIS) for optimization of a localized detector (tally) region (e.g., flux, dose, or reaction rate at a particular location) and (2) Forward Weighted CADIS (FW-CADIS) for optimizing distributions (e.g., mesh tallies over all or part of the problem space) or multiple localized detector regions (e.g., simultaneous optimization of two or moremore » localized tally regions). The two methods have been implemented and automated in both the MAVRIC sequence of SCALE 6 and ADVANTG, a code that works with the MCNP code. As implemented, the methods utilize the results of approximate, fast-running 3-D discrete ordinates transport calculations (with the Denovo code) to generate consistent space- and energy-dependent source and transport (weight windows) biasing parameters. These methods and codes have been applied to many relevant and challenging problems, including calculations of PWR ex-core thermal detector response, dose rates throughout an entire PWR facility, site boundary dose from arrays of commercial spent fuel storage casks, radiation fields for criticality accident alarm system placement, and detector response for special nuclear material detection scenarios and nuclear well-logging tools. Substantial computational speed-ups, generally O(102-4), have been realized for all applications to date. This paper provides a brief review of the methods, their implementation, results of their application, and current development activities, as well as a considerable list of references for readers seeking more information about the methods and/or their applications.« less

Python-Assisted MODFLOW Application and Code Development

NASA Astrophysics Data System (ADS)

Langevin, C.

2013-12-01

The U.S. Geological Survey (USGS) has a long history of developing and maintaining free, open-source software for hydrological investigations. The MODFLOW program is one of the most popular hydrologic simulation programs released by the USGS, and it is considered to be the most widely used groundwater flow simulation code. MODFLOW was written using a modular design and a procedural FORTRAN style, which resulted in code that could be understood, modified, and enhanced by many hydrologists. The code is fast, and because it uses standard FORTRAN it can be run on most operating systems. Most MODFLOW users rely on proprietary graphical user interfaces for constructing models and viewing model results. Some recent efforts, however, have focused on construction of MODFLOW models using open-source Python scripts. Customizable Python packages, such as FloPy (https://code.google.com/p/flopy), can be used to generate input files, read simulation results, and visualize results in two and three dimensions. Automating this sequence of steps leads to models that can be reproduced directly from original data and rediscretized in space and time. Python is also being used in the development and testing of new MODFLOW functionality. New packages and numerical formulations can be quickly prototyped and tested first with Python programs before implementation in MODFLOW. This is made possible by the flexible object-oriented design capabilities available in Python, the ability to call FORTRAN code from Python, and the ease with which linear systems of equations can be solved using SciPy, for example. Once new features are added to MODFLOW, Python can then be used to automate comprehensive regression testing and ensure reliability and accuracy of new versions prior to release.

Experience with a vectorized general circulation weather model on Star-100

NASA Technical Reports Server (NTRS)

Soll, D. B.; Habra, N. R.; Russell, G. L.

1977-01-01

A version of an atmospheric general circulation model was vectorized to run on a CDC STAR 100. The numerical model was coded and run in two different vector languages, CDC and LRLTRAN. A factor of 10 speed improvement over an IBM 360/95 was realized. Efficient use of the STAR machine required some redesigning of algorithms and logic. This precludes the application of vectorizing compilers on the original scalar code to achieve the same results. Vector languages permit a more natural and efficient formulation for such numerical codes.

Modulation and coding for fast fading mobile satellite communication channels

NASA Technical Reports Server (NTRS)

Mclane, P. J.; Wittke, P. H.; Smith, W. S.; Lee, A.; Ho, P. K. M.; Loo, C.

1988-01-01

The performance of Gaussian baseband filtered minimum shift keying (GMSK) using differential detection in fast Rician fading, with a novel treatment of the inherent intersymbol interference (ISI) leading to an exact solution is discussed. Trellis-coded differentially coded phase shift keying (DPSK) with a convolutional interleaver is considered. The channel is the Rician Channel with the line-of-sight component subject to a lognormal transformation.

Improved Algorithms Speed It Up for Codes

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

Hazi, A

2005-09-20

Huge computers, huge codes, complex problems to solve. The longer it takes to run a code, the more it costs. One way to speed things up and save time and money is through hardware improvements--faster processors, different system designs, bigger computers. But another side of supercomputing can reap savings in time and speed: software improvements to make codes--particularly the mathematical algorithms that form them--run faster and more efficiently. Speed up math? Is that really possible? According to Livermore physicist Eugene Brooks, the answer is a resounding yes. ''Sure, you get great speed-ups by improving hardware,'' says Brooks, the deputy leadermore » for Computational Physics in N Division, which is part of Livermore's Physics and Advanced Technologies (PAT) Directorate. ''But the real bonus comes on the software side, where improvements in software can lead to orders of magnitude improvement in run times.'' Brooks knows whereof he speaks. Working with Laboratory physicist Abraham Szoeke and others, he has been instrumental in devising ways to shrink the running time of what has, historically, been a tough computational nut to crack: radiation transport codes based on the statistical or Monte Carlo method of calculation. And Brooks is not the only one. Others around the Laboratory, including physicists Andrew Williamson, Randolph Hood, and Jeff Grossman, have come up with innovative ways to speed up Monte Carlo calculations using pure mathematics.« less

Effects of general, specific and combined warm-up on explosive muscular performance

PubMed Central

Henriquez–Olguín, C; Beltrán, AR; Ramírez, MA; Labarca, C; Cornejo, M; Álvarez, C; Ramírez-Campillo, R

2015-01-01

The purpose of this study was to compare the acute effects of general, specific and combined warm-up (WU) on explosive performance. Healthy male (n = 10) subjects participated in six WU protocols in a crossover randomized study design. Protocols were: passive rest (PR; 15 min of passive rest), running (Run; 5 min of running at 70% of maximum heart rate), stretching (STR; 5 min of static stretching exercise), jumping [Jump; 5 min of jumping exercises – 3x8 countermovement jumps (CMJ) and 3x8 drop jumps from 60 cm (DJ60)], and combined (COM; protocols Run+STR+Jump combined). Immediately before and after each WU, subjects were assessed for explosive concentric-only (i.e. squat jump – SJ), slow stretch-shortening cycle (i.e. CMJ), fast stretch-shortening cycle (i.e. DJ60) and contact time (CT) muscle performance. PR significantly reduced SJ performance (p =0.007). Run increased SJ (p =0.0001) and CMJ (p =0.002). STR increased CMJ (p =0.048). Specific WU (i.e. Jump) increased SJ (p =0.001), CMJ (p =0.028) and DJ60 (p =0.006) performance. COM increased CMJ performance (p =0.006). Jump was superior in SJ performance vs. PR (p =0.001). Jump reduced (p =0.03) CT in DJ60. In conclusion, general, specific and combined WU increase slow stretch-shortening cycle (SSC) muscle performance, but only specific WU increases fast SSC muscle performance. Therefore, to increase fast SSC performance, specific fast SSC muscle actions must be included during the WU. PMID:26060335

Effects of changing speed on knee and ankle joint load during walking and running.

PubMed

de David, Ana Cristina; Carpes, Felipe Pivetta; Stefanyshyn, Darren

2015-01-01

Joint moments can be used as an indicator of joint loading and have potential application for sports performance and injury prevention. The effects of changing walking and running speeds on joint moments for the different planes of motion still are debatable. Here, we compared knee and ankle moments during walking and running at different speeds. Data were collected from 11 recreational male runners to determine knee and ankle joint moments during different conditions. Conditions include walking at a comfortable speed (self-selected pacing), fast walking (fastest speed possible), slow running (speed corresponding to 30% slower than running) and running (at 4 m · s(-1) ± 10%). A different joint moment pattern was observed between walking and running. We observed a general increase in joint load for sagittal and frontal planes as speed increased, while the effects of speed were not clear in the transverse plane moments. Although differences tend to be more pronounced when gait changed from walking to running, the peak moments, in general, increased when speed increased from comfortable walking to fast walking and from slow running to running mainly in the sagittal and frontal planes. Knee flexion moment was higher in walking than in running due to larger knee extension. Results suggest caution when recommending walking over running in an attempt to reduce knee joint loading. The different effects of speed increments during walking and running should be considered with regard to the prevention of injuries and for rehabilitation purposes.

FBCOT: a fast block coding option for JPEG 2000

NASA Astrophysics Data System (ADS)

Taubman, David; Naman, Aous; Mathew, Reji

2017-09-01

Based on the EBCOT algorithm, JPEG 2000 finds application in many fields, including high performance scientific, geospatial and video coding applications. Beyond digital cinema, JPEG 2000 is also attractive for low-latency video communications. The main obstacle for some of these applications is the relatively high computational complexity of the block coder, especially at high bit-rates. This paper proposes a drop-in replacement for the JPEG 2000 block coding algorithm, achieving much higher encoding and decoding throughputs, with only modest loss in coding efficiency (typically < 0.5dB). The algorithm provides only limited quality/SNR scalability, but offers truly reversible transcoding to/from any standard JPEG 2000 block bit-stream. The proposed FAST block coder can be used with EBCOT's post-compression RD-optimization methodology, allowing a target compressed bit-rate to be achieved even at low latencies, leading to the name FBCOT (Fast Block Coding with Optimized Truncation).

Segmentation, dynamic storage, and variable loading on CDC equipment

NASA Technical Reports Server (NTRS)

Tiffany, S. H.

1980-01-01

Techniques for varying the segmented load structure of a program and for varying the dynamic storage allocation, depending upon whether a batch type or interactive type run is desired, are explained and demonstrated. All changes are based on a single data input to the program. The techniques involve: code within the program to suppress scratch pad input/output (I/O) for a batch run or translate the in-core data storage area from blank common to the end-of-code+1 address of a particular segment for an interactive run; automatic editing of the segload directives prior to loading, based upon data input to the program, to vary the structure of the load for interactive and batch runs; and automatic editing of the load map to determine the initial addresses for in core data storage for an interactive run.

Employing multi-GPU power for molecular dynamics simulation: an extension of GALAMOST

NASA Astrophysics Data System (ADS)

Zhu, You-Liang; Pan, Deng; Li, Zhan-Wei; Liu, Hong; Qian, Hu-Jun; Zhao, Yang; Lu, Zhong-Yuan; Sun, Zhao-Yan

2018-04-01

We describe the algorithm of employing multi-GPU power on the basis of Message Passing Interface (MPI) domain decomposition in a molecular dynamics code, GALAMOST, which is designed for the coarse-grained simulation of soft matters. The code of multi-GPU version is developed based on our previous single-GPU version. In multi-GPU runs, one GPU takes charge of one domain and runs single-GPU code path. The communication between neighbouring domains takes a similar algorithm of CPU-based code of LAMMPS, but is optimised specifically for GPUs. We employ a memory-saving design which can enlarge maximum system size at the same device condition. An optimisation algorithm is employed to prolong the update period of neighbour list. We demonstrate good performance of multi-GPU runs on the simulation of Lennard-Jones liquid, dissipative particle dynamics liquid, polymer and nanoparticle composite, and two-patch particles on workstation. A good scaling of many nodes on cluster for two-patch particles is presented.

Density-based parallel skin lesion border detection with webCL

PubMed Central

2015-01-01

Background Dermoscopy is a highly effective and noninvasive imaging technique used in diagnosis of melanoma and other pigmented skin lesions. Many aspects of the lesion under consideration are defined in relation to the lesion border. This makes border detection one of the most important steps in dermoscopic image analysis. In current practice, dermatologists often delineate borders through a hand drawn representation based upon visual inspection. Due to the subjective nature of this technique, intra- and inter-observer variations are common. Because of this, the automated assessment of lesion borders in dermoscopic images has become an important area of study. Methods Fast density based skin lesion border detection method has been implemented in parallel with a new parallel technology called WebCL. WebCL utilizes client side computing capabilities to use available hardware resources such as multi cores and GPUs. Developed WebCL-parallel density based skin lesion border detection method runs efficiently from internet browsers. Results Previous research indicates that one of the highest accuracy rates can be achieved using density based clustering techniques for skin lesion border detection. While these algorithms do have unfavorable time complexities, this effect could be mitigated when implemented in parallel. In this study, density based clustering technique for skin lesion border detection is parallelized and redesigned to run very efficiently on the heterogeneous platforms (e.g. tablets, SmartPhones, multi-core CPUs, GPUs, and fully-integrated Accelerated Processing Units) by transforming the technique into a series of independent concurrent operations. Heterogeneous computing is adopted to support accessibility, portability and multi-device use in the clinical settings. For this, we used WebCL, an emerging technology that enables a HTML5 Web browser to execute code in parallel for heterogeneous platforms. We depicted WebCL and our parallel algorithm design. In addition, we tested parallel code on 100 dermoscopy images and showed the execution speedups with respect to the serial version. Results indicate that parallel (WebCL) version and serial version of density based lesion border detection methods generate the same accuracy rates for 100 dermoscopy images, in which mean of border error is 6.94%, mean of recall is 76.66%, and mean of precision is 99.29% respectively. Moreover, WebCL version's speedup factor for 100 dermoscopy images' lesion border detection averages around ~491.2. Conclusions When large amount of high resolution dermoscopy images considered in a usual clinical setting along with the critical importance of early detection and diagnosis of melanoma before metastasis, the importance of fast processing dermoscopy images become obvious. In this paper, we introduce WebCL and the use of it for biomedical image processing applications. WebCL is a javascript binding of OpenCL, which takes advantage of GPU computing from a web browser. Therefore, WebCL parallel version of density based skin lesion border detection introduced in this study can supplement expert dermatologist, and aid them in early diagnosis of skin lesions. While WebCL is currently an emerging technology, a full adoption of WebCL into the HTML5 standard would allow for this implementation to run on a very large set of hardware and software systems. WebCL takes full advantage of parallel computational resources including multi-cores and GPUs on a local machine, and allows for compiled code to run directly from the Web Browser. PMID:26423836

Density-based parallel skin lesion border detection with webCL.

PubMed

Lemon, James; Kockara, Sinan; Halic, Tansel; Mete, Mutlu

2015-01-01

Dermoscopy is a highly effective and noninvasive imaging technique used in diagnosis of melanoma and other pigmented skin lesions. Many aspects of the lesion under consideration are defined in relation to the lesion border. This makes border detection one of the most important steps in dermoscopic image analysis. In current practice, dermatologists often delineate borders through a hand drawn representation based upon visual inspection. Due to the subjective nature of this technique, intra- and inter-observer variations are common. Because of this, the automated assessment of lesion borders in dermoscopic images has become an important area of study. Fast density based skin lesion border detection method has been implemented in parallel with a new parallel technology called WebCL. WebCL utilizes client side computing capabilities to use available hardware resources such as multi cores and GPUs. Developed WebCL-parallel density based skin lesion border detection method runs efficiently from internet browsers. Previous research indicates that one of the highest accuracy rates can be achieved using density based clustering techniques for skin lesion border detection. While these algorithms do have unfavorable time complexities, this effect could be mitigated when implemented in parallel. In this study, density based clustering technique for skin lesion border detection is parallelized and redesigned to run very efficiently on the heterogeneous platforms (e.g. tablets, SmartPhones, multi-core CPUs, GPUs, and fully-integrated Accelerated Processing Units) by transforming the technique into a series of independent concurrent operations. Heterogeneous computing is adopted to support accessibility, portability and multi-device use in the clinical settings. For this, we used WebCL, an emerging technology that enables a HTML5 Web browser to execute code in parallel for heterogeneous platforms. We depicted WebCL and our parallel algorithm design. In addition, we tested parallel code on 100 dermoscopy images and showed the execution speedups with respect to the serial version. Results indicate that parallel (WebCL) version and serial version of density based lesion border detection methods generate the same accuracy rates for 100 dermoscopy images, in which mean of border error is 6.94%, mean of recall is 76.66%, and mean of precision is 99.29% respectively. Moreover, WebCL version's speedup factor for 100 dermoscopy images' lesion border detection averages around ~491.2. When large amount of high resolution dermoscopy images considered in a usual clinical setting along with the critical importance of early detection and diagnosis of melanoma before metastasis, the importance of fast processing dermoscopy images become obvious. In this paper, we introduce WebCL and the use of it for biomedical image processing applications. WebCL is a javascript binding of OpenCL, which takes advantage of GPU computing from a web browser. Therefore, WebCL parallel version of density based skin lesion border detection introduced in this study can supplement expert dermatologist, and aid them in early diagnosis of skin lesions. While WebCL is currently an emerging technology, a full adoption of WebCL into the HTML5 standard would allow for this implementation to run on a very large set of hardware and software systems. WebCL takes full advantage of parallel computational resources including multi-cores and GPUs on a local machine, and allows for compiled code to run directly from the Web Browser.

Performance tuning of N-body codes on modern microprocessors: I. Direct integration with a hermite scheme on x86_64 architecture

NASA Astrophysics Data System (ADS)

Nitadori, Keigo; Makino, Junichiro; Hut, Piet

2006-12-01

The main performance bottleneck of gravitational N-body codes is the force calculation between two particles. We have succeeded in speeding up this pair-wise force calculation by factors between 2 and 10, depending on the code and the processor on which the code is run. These speed-ups were obtained by writing highly fine-tuned code for x86_64 microprocessors. Any existing N-body code, running on these chips, can easily incorporate our assembly code programs. In the current paper, we present an outline of our overall approach, which we illustrate with one specific example: the use of a Hermite scheme for a direct N2 type integration on a single 2.0 GHz Athlon 64 processor, for which we obtain an effective performance of 4.05 Gflops, for double-precision accuracy. In subsequent papers, we will discuss other variations, including the combinations of N log N codes, single-precision implementations, and performance on other microprocessors.

X-Antenna: A graphical interface for antenna analysis codes

NASA Technical Reports Server (NTRS)

Goldstein, B. L.; Newman, E. H.; Shamansky, H. T.

1995-01-01

This report serves as the user's manual for the X-Antenna code. X-Antenna is intended to simplify the analysis of antennas by giving the user graphical interfaces in which to enter all relevant antenna and analysis code data. Essentially, X-Antenna creates a Motif interface to the user's antenna analysis codes. A command-file allows new antennas and codes to be added to the application. The menu system and graphical interface screens are created dynamically to conform to the data in the command-file. Antenna data can be saved and retrieved from disk. X-Antenna checks all antenna and code values to ensure they are of the correct type, writes an output file, and runs the appropriate antenna analysis code. Volumetric pattern data may be viewed in 3D space with an external viewer run directly from the application. Currently, X-Antenna includes analysis codes for thin wire antennas (dipoles, loops, and helices), rectangular microstrip antennas, and thin slot antennas.

User's and test case manual for FEMATS

NASA Technical Reports Server (NTRS)

Chatterjee, Arindam; Volakis, John; Nurnberger, Mike; Natzke, John

1995-01-01

The FEMATS program incorporates first-order edge-based finite elements and vector absorbing boundary conditions into the scattered field formulation for computation of the scattering from three-dimensional geometries. The code has been validated extensively for a large class of geometries containing inhomogeneities and satisfying transition conditions. For geometries that are too large for the workstation environment, the FEMATS code has been optimized to run on various supercomputers. Currently, FEMATS has been configured to run on the HP 9000 workstation, vectorized for the Cray Y-MP, and parallelized to run on the Kendall Square Research (KSR) architecture and the Intel Paragon.

INDDGO: Integrated Network Decomposition & Dynamic programming for Graph Optimization

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

Groer, Christopher S; Sullivan, Blair D; Weerapurage, Dinesh P

2012-10-01

It is well-known that dynamic programming algorithms can utilize tree decompositions to provide a way to solve some \\emph{NP}-hard problems on graphs where the complexity is polynomial in the number of nodes and edges in the graph, but exponential in the width of the underlying tree decomposition. However, there has been relatively little computational work done to determine the practical utility of such dynamic programming algorithms. We have developed software to construct tree decompositions using various heuristics and have created a fast, memory-efficient dynamic programming implementation for solving maximum weighted independent set. We describe our software and the algorithms wemore » have implemented, focusing on memory saving techniques for the dynamic programming. We compare the running time and memory usage of our implementation with other techniques for solving maximum weighted independent set, including a commercial integer programming solver and a semi-definite programming solver. Our results indicate that it is possible to solve some instances where the underlying decomposition has width much larger than suggested by the literature. For certain types of problems, our dynamic programming code runs several times faster than these other methods.« less

Benchmarking NNWSI flow and transport codes: COVE 1 results

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

Hayden, N.K.

1985-06-01

The code verification (COVE) activity of the Nevada Nuclear Waste Storage Investigations (NNWSI) Project is the first step in certification of flow and transport codes used for NNWSI performance assessments of a geologic repository for disposing of high-level radioactive wastes. The goals of the COVE activity are (1) to demonstrate and compare the numerical accuracy and sensitivity of certain codes, (2) to identify and resolve problems in running typical NNWSI performance assessment calculations, and (3) to evaluate computer requirements for running the codes. This report describes the work done for COVE 1, the first step in benchmarking some of themore » codes. Isothermal calculations for the COVE 1 benchmarking have been completed using the hydrologic flow codes SAGUARO, TRUST, and GWVIP; the radionuclide transport codes FEMTRAN and TRUMP; and the coupled flow and transport code TRACR3D. This report presents the results of three cases of the benchmarking problem solved for COVE 1, a comparison of the results, questions raised regarding sensitivities to modeling techniques, and conclusions drawn regarding the status and numerical sensitivities of the codes. 30 refs.« less

Alternate operating scenarios for NDCX-II

NASA Astrophysics Data System (ADS)

Sharp, W. M.; Friedman, A.; Grote, D. P.; Cohen, R. H.; Lund, S. M.; Vay, J.-L.; Waldron, W. L.

2014-01-01

NDCX-II is a newly completed accelerator facility at LBNL, built to study ion-heated warm dense matter, as well as aspects of ion-driven targets and intense-beam dynamics for inertial-fusion energy. The baseline design calls for using 12 induction cells to accelerate 30-50 nC of Li+ ions to 1.2 MeV. During commissioning, though, we plan to extend the source lifetime by extracting less total charge. Over time, we expect that NDCX-II will be upgraded to substantially higher energies, necessitating the use of heavier ions to keep a suitable deposition range in targets. For operational flexibility, the option of using a helium plasma source is also being investigated. Each of these options requires development of an alternate acceleration schedule. The schedules here are worked out with a fast-running 1-D particle-in-cell code ASP.

Program For Evaluation Of Reliability Of Ceramic Parts

NASA Technical Reports Server (NTRS)

Nemeth, N.; Janosik, L. A.; Gyekenyesi, J. P.; Powers, Lynn M.

1996-01-01

CARES/LIFE predicts probability of failure of monolithic ceramic component as function of service time. Assesses risk that component fractures prematurely as result of subcritical crack growth (SCG). Effect of proof testing of components prior to service also considered. Coupled to such commercially available finite-element programs as ANSYS, ABAQUS, MARC, MSC/NASTRAN, and COSMOS/M. Also retains all capabilities of previous CARES code, which includes estimation of fast-fracture component reliability and Weibull parameters from inert strength (without SCG contributing to failure) specimen data. Estimates parameters that characterize SCG from specimen data as well. Written in ANSI FORTRAN 77 to be machine-independent. Program runs on any computer in which sufficient addressable memory (at least 8MB) and FORTRAN 77 compiler available. For IBM-compatible personal computer with minimum 640K memory, limited program available (CARES/PC, COSMIC number LEW-15248).

Online polarimetry of the Nuclotron internal deuteron and proton beams

NASA Astrophysics Data System (ADS)

Isupov, A. Yu

2017-12-01

The spin studies at Nuclotron require fast and precise determination of the deuteron and proton beam polarization. For these purposes new powerful VME-based data acquisition (DAQ) system has been designed for the Deuteron Spin Structure setup placed at the Nuclotron Internal Target Station. The DAQ system is built using the netgraph-based data acquisition and processing framework ngdp. The software dealing with VME hardware is a set of netgraph nodes in form of the loadable kernel modules, so works in the operating system kernel context. The specific for current implementation nodes and user context utilities are described. The online events representation by ROOT classes allows us to generalize code for histograms filling and polarization calculations. The DAQ system was successfully used during 53rd and 54th Nuclotron runs, and their suitability for online polarimetry is demonstrated.

Faster R-CNN: Towards Real-Time Object Detection with Region Proposal Networks.

PubMed

Ren, Shaoqing; He, Kaiming; Girshick, Ross; Sun, Jian

2017-06-01

State-of-the-art object detection networks depend on region proposal algorithms to hypothesize object locations. Advances like SPPnet [1] and Fast R-CNN [2] have reduced the running time of these detection networks, exposing region proposal computation as a bottleneck. In this work, we introduce a Region Proposal Network (RPN) that shares full-image convolutional features with the detection network, thus enabling nearly cost-free region proposals. An RPN is a fully convolutional network that simultaneously predicts object bounds and objectness scores at each position. The RPN is trained end-to-end to generate high-quality region proposals, which are used by Fast R-CNN for detection. We further merge RPN and Fast R-CNN into a single network by sharing their convolutional features-using the recently popular terminology of neural networks with 'attention' mechanisms, the RPN component tells the unified network where to look. For the very deep VGG-16 model [3] , our detection system has a frame rate of 5 fps (including all steps) on a GPU, while achieving state-of-the-art object detection accuracy on PASCAL VOC 2007, 2012, and MS COCO datasets with only 300 proposals per image. In ILSVRC and COCO 2015 competitions, Faster R-CNN and RPN are the foundations of the 1st-place winning entries in several tracks. Code has been made publicly available.

The Consequences of Alfven Waves and Parallel Potential Drops in the Auroral Zone

NASA Technical Reports Server (NTRS)

Schriver, David

2003-01-01

The goal of this research is to examine the causes of field-aligned plasma acceleration in the auroral zone using satellite data and numerical simulations. A primary question to be addressed is what causes the field-aligned acceleration of electrons (leading to precipitation) and ions (leading to upwelling ions) in the auroral zone. Data from the Fast Auroral SnapshoT (FAST) and Polar satellites is used when the two satellites are in approximate magnetic conjunction and are in the auroral region. FAST is at relatively low altitudes and samples plasma in the midst of the auroral acceleration region while Polar is at much higher altitudes and can measure plasmas and waves propagating towards the Earth. Polar can determine the sources of energy streaming earthward from the magnetotail, either in the form of field-aligned currents, electromagnetic waves or kinetic particle energy, that ultimately leads to the acceleration of plasma in the auroral zone. After identifying and examining several events, numerical simulations are run that bridges the spatial region between the two satellites. The code is a one-dimensional, long system length particle in cell simulation that has been developed to model the auroral region. A main goal of this research project is to include Alfven waves in the simulation to examine how these waves can accelerate plasma in the auroral zone.

TH-A-19A-08: Intel Xeon Phi Implementation of a Fast Multi-Purpose Monte Carlo Simulation for Proton Therapy

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

Souris, K; Lee, J; Sterpin, E

2014-06-15

Purpose: Recent studies have demonstrated the capability of graphics processing units (GPUs) to compute dose distributions using Monte Carlo (MC) methods within clinical time constraints. However, GPUs have a rigid vectorial architecture that favors the implementation of simplified particle transport algorithms, adapted to specific tasks. Our new, fast, and multipurpose MC code, named MCsquare, runs on Intel Xeon Phi coprocessors. This technology offers 60 independent cores, and therefore more flexibility to implement fast and yet generic MC functionalities, such as prompt gamma simulations. Methods: MCsquare implements several models and hence allows users to make their own tradeoff between speed andmore » accuracy. A 200 MeV proton beam is simulated in a heterogeneous phantom using Geant4 and two configurations of MCsquare. The first one is the most conservative and accurate. The method of fictitious interactions handles the interfaces and secondary charged particles emitted in nuclear interactions are fully simulated. The second, faster configuration simplifies interface crossings and simulates only secondary protons after nuclear interaction events. Integral depth-dose and transversal profiles are compared to those of Geant4. Moreover, the production profile of prompt gammas is compared to PENH results. Results: Integral depth dose and transversal profiles computed by MCsquare and Geant4 are within 3%. The production of secondaries from nuclear interactions is slightly inaccurate at interfaces for the fastest configuration of MCsquare but this is unlikely to have any clinical impact. The computation time varies between 90 seconds for the most conservative settings to merely 59 seconds in the fastest configuration. Finally prompt gamma profiles are also in very good agreement with PENH results. Conclusion: Our new, fast, and multi-purpose Monte Carlo code simulates prompt gammas and calculates dose distributions in less than a minute, which complies with clinical time constraints. It has been successfully validated with Geant4. This work has been financialy supported by InVivoIGT, a public/private partnership between UCL and IBA.« less

Fast-ion D(alpha) measurements and simulations in DIII-D

NASA Astrophysics Data System (ADS)

Luo, Yadong

The fast-ion Dalpha diagnostic measures the Doppler-shifted Dalpha light emitted by neutralized fast ions. For a favorable viewing geometry, the bright interferences from beam neutrals, halo neutrals, and edge neutrals span over a small wavelength range around the Dalpha rest wavelength and are blocked by a vertical bar at the exit focal plane of the spectrometer. Background subtraction and fitting techniques eliminate various contaminants in the spectrum. Fast-ion data are acquired with a time evolution of ˜1 ms, spatial resolution of ˜5 cm, and energy resolution of ˜10 keV. A weighted Monte Carlo simulation code models the fast-ion Dalpha spectra based on the fast-ion distribution function from other sources. In quiet plasmas, the spectral shape is in excellent agreement and absolute magnitude also has reasonable agreement. The fast-ion D alpha signal has the expected dependencies on plasma and neutral beam parameters. The neutral particle diagnostic and neutron diagnostic corroborate the fast-ion Dalpha measurements. The relative spatial profile is in agreement with the simulated profile based on the fast-ion distribution function from the TRANSP analysis code. During ion cyclotron heating, fast ions with high perpendicular energy are accelerated, while those with low perpendicular energy are barely affected. The spatial profile is compared with the simulated profiles based on the fast-ion distribution functions from the CQL Fokker-Planck code. In discharges with Alfven instabilities, both the spatial profile and spectral shape suggests that fast ions are redistributed. The flattened fast-ion Dalpha profile is in agreement with the fast-ion pressure profile.

On Your Mark! Get Set! Go!

ERIC Educational Resources Information Center

Rowland, Veronica

2006-01-01

This article describes how second- and third-grade students joined their teacher, Mary Ann McTiernan, a marathon runner from Cape Town, South Africa, in a one-mile run every Thursday morning while she was training. Mary Ann's students had been asking, "Where do you run?" "How far do you go?" "How fast can you run?"…

Investigation of HZETRN 2010 as a Tool for Single Event Effect Qualification of Avionics Systems

NASA Technical Reports Server (NTRS)

Rojdev, Kristina; Atwell, William; Boeder, Paul; Koontz, Steve

2014-01-01

NASA's future missions are focused on deep space for human exploration that do not provide a simple emergency return to Earth. In addition, the deep space environment contains a constant background Galactic Cosmic Ray (GCR) radiation exposure, as well as periodic Solar Particle Events (SPEs) that can produce intense amounts of radiation in a short amount of time. Given these conditions, it is important that the avionics systems for deep space human missions are not susceptible to Single Event Effects (SEE) that can occur from radiation interactions with electronic components. The typical process to minimizing SEE effects is through using heritage hardware and extensive testing programs that are very costly. Previous work by Koontz, et al. [1] utilized an analysis-based method for investigating electronic component susceptibility. In their paper, FLUKA, a Monte Carlo transport code, was used to calculate SEE and single event upset (SEU) rates. This code was then validated against in-flight data. In addition, CREME-96, a deterministic code, was also compared with FLUKA and in-flight data. However, FLUKA has a long run-time (on the order of days), and CREME-96 has not been updated in several years. This paper will investigate the use of HZETRN 2010, a deterministic transport code developed at NASA Langley Research Center, as another tool that can be used to analyze SEE and SEU rates. The benefits to using HZETRN over FLUKA and CREME-96 are that it has a very fast run time (on the order of minutes) and has been shown to be of similar accuracy as other deterministic and Monte Carlo codes when considering dose [2, 3, 4]. The 2010 version of HZETRN has updated its treatment of secondary neutrons and thus has improved its accuracy over previous versions. In this paper, the Linear Energy Transfer (LET) spectra are of interest rather than the total ionizing dose. Therefore, the LET spectra output from HZETRN 2010 will be compared with the FLUKA and in-flight data to validate HZETRN 2010 as a computational tool for SEE qualification by analysis. Furthermore, extrapolation of these data to interplanetary environments at 1 AU will be investigated to determine whether HZETRN 2010 can be used successfully and confidently for deep space mission analyses.

Wind turbine design codes: A comparison of the structural response

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

Buhl, M.L. Jr.; Wright, A.D.; Pierce, K.G.

2000-03-01

The National Wind Technology Center (NWTC) of the National Renewable Energy Laboratory is continuing a comparison of several computer codes used in the design and analysis of wind turbines. The second part of this comparison determined how well the programs predict the structural response of wind turbines. In this paper, the authors compare the structural response for four programs: ADAMS, BLADED, FAST{_}AD, and YawDyn. ADAMS is a commercial, multibody-dynamics code from Mechanical Dynamics, Inc. BLADED is a commercial, performance and structural-response code from Garrad Hassan and Partners Limited. FAST{_}AD is a structural-response code developed by Oregon State University and themore » University of Utah for the NWTC. YawDyn is a structural-response code developed by the University of Utah for the NWTC. ADAMS, FAST{_}AD, and YawDyn use the University of Utah's AeroDyn subroutine package for calculating aerodynamic forces. Although errors were found in all the codes during this study, once they were fixed, the codes agreed surprisingly well for most of the cases and configurations that were evaluated. One unresolved discrepancy between BLADED and the AeroDyn-based codes was when there was blade and/or teeter motion in addition to a large yaw error.« less

DOUBLE code simulations of emissivities of fast neutrals for different plasma observation view-lines of neutral particle analyzers on the COMPASS tokamak

NASA Astrophysics Data System (ADS)

Mitosinkova, K.; Tomes, M.; Stockel, J.; Varju, J.; Stano, M.

2018-03-01

Neutral particle analyzers (NPA) measure line-integrated energy spectra of fast neutral atoms escaping the tokamak plasma, which are a product of charge-exchange (CX) collisions of plasma ions with background neutrals. They can observe variations in the ion temperature T i of non-thermal fast ions created by additional plasma heating. However, the plasma column which a fast atom has to pass through must be sufficiently short in comparison with the fast atom’s mean-free-path. Tokamak COMPASS is currently equipped with one NPA installed at a tangential mid-plane port. This orientation is optimal for observing non-thermal fast ions. However, in this configuration the signal at energies useful for T i derivation is lost in noise due to the too long fast atoms’ trajectories. Thus, a second NPA is planned to be connected for the purpose of measuring T i. We analyzed different possible view-lines (perpendicular mid-plane, tangential mid-plane, and top view) for the second NPA using the DOUBLE Monte-Carlo code and compared the results with the performance of the present NPA with tangential orientation. The DOUBLE code provides fast-atoms’ emissivity functions along the NPA view-line. The position of the median of these emissivity functions is related to the location from where the measured signal originates. Further, we compared the difference between the real central T i used as a DOUBLE code input and the T iCX derived from the exponential decay of simulated energy spectra. The advantages and disadvantages of each NPA location are discussed.

TIGER: Turbomachinery interactive grid generation

NASA Technical Reports Server (NTRS)

Soni, Bharat K.; Shih, Ming-Hsin; Janus, J. Mark

1992-01-01

A three dimensional, interactive grid generation code, TIGER, is being developed for analysis of flows around ducted or unducted propellers. TIGER is a customized grid generator that combines new technology with methods from general grid generation codes. The code generates multiple block, structured grids around multiple blade rows with a hub and shroud for either C grid or H grid topologies. The code is intended for use with a Euler/Navier-Stokes solver also being developed, but is general enough for use with other flow solvers. TIGER features a silicon graphics interactive graphics environment that displays a pop-up window, graphics window, and text window. The geometry is read as a discrete set of points with options for several industrial standard formats and NASA standard formats. Various splines are available for defining the surface geometries. Grid generation is done either interactively or through a batch mode operation using history files from a previously generated grid. The batch mode operation can be done either with a graphical display of the interactive session or with no graphics so that the code can be run on another computer system. Run time can be significantly reduced by running on a Cray-YMP.

Transient dynamics capability at Sandia National Laboratories

NASA Technical Reports Server (NTRS)

Attaway, Steven W.; Biffle, Johnny H.; Sjaardema, G. D.; Heinstein, M. W.; Schoof, L. A.

1993-01-01

A brief overview of the transient dynamics capabilities at Sandia National Laboratories, with an emphasis on recent new developments and current research is presented. In addition, the Sandia National Laboratories (SNL) Engineering Analysis Code Access System (SEACAS), which is a collection of structural and thermal codes and utilities used by analysts at SNL, is described. The SEACAS system includes pre- and post-processing codes, analysis codes, database translation codes, support libraries, Unix shell scripts for execution, and an installation system. SEACAS is used at SNL on a daily basis as a production, research, and development system for the engineering analysts and code developers. Over the past year, approximately 190 days of CPU time were used by SEACAS codes on jobs running from a few seconds up to two and one-half days of CPU time. SEACAS is running on several different systems at SNL including Cray Unicos, Hewlett Packard PH-UX, Digital Equipment Ultrix, and Sun SunOS. An overview of SEACAS, including a short description of the codes in the system, are presented. Abstracts and references for the codes are listed at the end of the report.

Simulation of LHC events on a millions threads

NASA Astrophysics Data System (ADS)

Childers, J. T.; Uram, T. D.; LeCompte, T. J.; Papka, M. E.; Benjamin, D. P.

2015-12-01

Demand for Grid resources is expected to double during LHC Run II as compared to Run I; the capacity of the Grid, however, will not double. The HEP community must consider how to bridge this computing gap by targeting larger compute resources and using the available compute resources as efficiently as possible. Argonne's Mira, the fifth fastest supercomputer in the world, can run roughly five times the number of parallel processes that the ATLAS experiment typically uses on the Grid. We ported Alpgen, a serial x86 code, to run as a parallel application under MPI on the Blue Gene/Q architecture. By analysis of the Alpgen code, we reduced the memory footprint to allow running 64 threads per node, utilizing the four hardware threads available per core on the PowerPC A2 processor. Event generation and unweighting, typically run as independent serial phases, are coupled together in a single job in this scenario, reducing intermediate writes to the filesystem. By these optimizations, we have successfully run LHC proton-proton physics event generation at the scale of a million threads, filling two-thirds of Mira.

Radiative corrections from heavy fast-roll fields during inflation

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

Jain, Rajeev Kumar; Sandora, McCullen; Sloth, Martin S., E-mail: jain@cp3.dias.sdu.dk, E-mail: sandora@cp3.dias.sdu.dk, E-mail: sloth@cp3.dias.sdu.dk

2015-06-01

We investigate radiative corrections to the inflaton potential from heavy fields undergoing a fast-roll phase transition. We find that a logarithmic one-loop correction to the inflaton potential involving this field can induce a temporary running of the spectral index. The induced running can be a short burst of strong running, which may be related to the observed anomalies on large scales in the cosmic microwave spectrum, or extend over many e-folds, sustaining an effectively constant running to be searched for in the future. We implement this in a general class of models, where effects are mediated through a heavy messengermore » field sitting in its minimum. Interestingly, within the present framework it is a generic outcome that a large running implies a small field model with a vanishing tensor-to-scalar ratio, circumventing the normal expectation that small field models typically lead to an unobservably small running of the spectral index. An observable level of tensor modes can also be accommodated, but, surprisingly, this requires running to be induced by a curvaton. If upcoming observations are consistent with a small tensor-to-scalar ratio as predicted by small field models of inflation, then the present study serves as an explicit example contrary to the general expectation that the running will be unobservable.« less

Radiative corrections from heavy fast-roll fields during inflation

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

Jain, Rajeev Kumar; Sandora, McCullen; Sloth, Martin S.

2015-06-09

We investigate radiative corrections to the inflaton potential from heavy fields undergoing a fast-roll phase transition. We find that a logarithmic one-loop correction to the inflaton potential involving this field can induce a temporary running of the spectral index. The induced running can be a short burst of strong running, which may be related to the observed anomalies on large scales in the cosmic microwave spectrum, or extend over many e-folds, sustaining an effectively constant running to be searched for in the future. We implement this in a general class of models, where effects are mediated through a heavy messengermore » field sitting in its minimum. Interestingly, within the present framework it is a generic outcome that a large running implies a small field model with a vanishing tensor-to-scalar ratio, circumventing the normal expectation that small field models typically lead to an unobservably small running of the spectral index. An observable level of tensor modes can also be accommodated, but, surprisingly, this requires running to be induced by a curvaton. If upcoming observations are consistent with a small tensor-to-scalar ratio as predicted by small field models of inflation, then the present study serves as an explicit example contrary to the general expectation that the running will be unobservable.« less

Development of Web Interfaces for Analysis Codes

NASA Astrophysics Data System (ADS)

Emoto, M.; Watanabe, T.; Funaba, H.; Murakami, S.; Nagayama, Y.; Kawahata, K.

Several codes have been developed to analyze plasma physics. However, most of them are developed to run on supercomputers. Therefore, users who typically use personal computers (PCs) find it difficult to use these codes. In order to facilitate the widespread use of these codes, a user-friendly interface is required. The authors propose Web interfaces for these codes. To demonstrate the usefulness of this approach, the authors developed Web interfaces for two analysis codes. One of them is for FIT developed by Murakami. This code is used to analyze the NBI heat deposition, etc. Because it requires electron density profiles, electron temperatures, and ion temperatures as polynomial expressions, those unfamiliar with the experiments find it difficult to use this code, especially visitors from other institutes. The second one is for visualizing the lines of force in the LHD (large helical device) developed by Watanabe. This code is used to analyze the interference caused by the lines of force resulting from the various structures installed in the vacuum vessel of the LHD. This code runs on PCs; however, it requires that the necessary parameters be edited manually. Using these Web interfaces, users can execute these codes interactively.

Concept of a Fast and Simple Atmospheric Radiative Transfer Model for Aerosol Retrieval

NASA Astrophysics Data System (ADS)

Seidel, Felix; Kokhanovsky, Alexander A.

2010-05-01

Radiative transfer modelling (RTM) is an indispensable tool for a number of applications, including astrophysics, climate studies and quantitative remote sensing. It simulates the attenuation of light through a translucent medium. Here, we look at the scattering and absorption of solar light on its way to the Earth's surface and back to space or back into a remote sensing instrument. RTM is regularly used in the framework of the so-called atmospheric correction to find properties of the surface. Further, RTM can be inverted to retrieve features of the atmosphere, such as the aerosol optical depth (AOD), for instance. Present-day RTM, such as 6S, MODTRAN, SHARM, RT3, SCIATRAN or RTMOM have errors of only a few percent, however they are rather slow and often not easy to use. We present here a concept for a fast and simple RTM model in the visible spectral range. It is using a blend of different existing RTM approaches with a special emphasis on fast approximative analytical equations and parametrizations. This concept may be helpful for efficient retrieval algorithms, which do not have to rely on the classic look-up-tables (LUT) approach. For example, it can be used to retrieve AOD without complex inversion procedures including multiple iterations. Naturally, there is always a trade-off between speed and modelling accuracy. The code can be run therefore in two different modes. The regular mode provides a reasonable ratio between speed and accuracy, while the optional mode is very fast but less accurate. The normal mode approximates the diffuse scattered light by calculating the first (single scattering) and second order of scattering according to the classical method of successive orders of scattering. The very fast mode calculates only the single scattering approximation, which does not need any slow numerical integration procedure, and uses a simple correction factor to account for multiple scattering. This factor is a parametrization of MODTRAN results, which provide a typical ratio between single and multiple scattered light. A comparison of the presented RTM concept to the widely accepted 6S RTM reveals errors of up to 10% in standard mode. This is acceptable for certain applications. The very fast mode may lead to errors of up to 30%, but it is still able to reproduce qualitatively the results of 6S. An experimental implementation of this RTM concept is written in the common IDL language. It is therefore very flexible and straightforward to be implemented into custom retrieval algorithms of the remote sensing community. The code might also be used to add an atmosphere on top of an existing vegetation-canopy or water RTM. Due to the ease of use of the RTM code and the comprehensibility of the internal equations, the concept might be useful for educational purposes as well. The very fast mode could be of interest for a real-time applications, such as an in-flight instrument performance check for airborne optical sensors. In the future, the concept can be extended to account for scattering according to Mie theory, polarization and gaseous absorption. It is expected that this would reduce the model error to 5% or less.

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.

On Why It Is Impossible to Prove that the BDX90 Dispatcher Implements a Time-sharing System

NASA Technical Reports Server (NTRS)

Boyer, R. S.; Moore, J. S.

1983-01-01

The Software Implemented Fault Tolerance SIFT system, is written in PASCAL except for about a page of machine code. The SIFT system implements a small time sharing system in which PASCAL programs for separate application tasks are executed according to a schedule with real time constraints. The PASCAL language has no provision for handling the notion of an interrupt such as the B930 clock interrupt. The PASCAL language also lacks the notion of running a PASCAL subroutine for a given amount of time, suspending it, saving away the suspension, and later activating the suspension. Machine code was used to overcome these inadequacies of PASCAL. Code which handles clock interrupts and suspends processes is called a dispatcher. The time sharing/virtual machine idea is completely destroyed by the reconfiguration task. After termination of the reconfiguration task, the tasks run by the dispatcher have no relation to those run before reconfiguration. It is impossible to view the dispatcher as a time-sharing system implementing virtual BDX930s running concurrently when one process can wipe out the others.

XMDS2: Fast, scalable simulation of coupled stochastic partial differential equations

NASA Astrophysics Data System (ADS)

Dennis, Graham R.; Hope, Joseph J.; Johnsson, Mattias T.

2013-01-01

XMDS2 is a cross-platform, GPL-licensed, open source package for numerically integrating initial value problems that range from a single ordinary differential equation up to systems of coupled stochastic partial differential equations. The equations are described in a high-level XML-based script, and the package generates low-level optionally parallelised C++ code for the efficient solution of those equations. It combines the advantages of high-level simulations, namely fast and low-error development, with the speed, portability and scalability of hand-written code. XMDS2 is a complete redesign of the XMDS package, and features support for a much wider problem space while also producing faster code. Program summaryProgram title: XMDS2 Catalogue identifier: AENK_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AENK_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 2 No. of lines in distributed program, including test data, etc.: 872490 No. of bytes in distributed program, including test data, etc.: 45522370 Distribution format: tar.gz Programming language: Python and C++. Computer: Any computer with a Unix-like system, a C++ compiler and Python. Operating system: Any Unix-like system; developed under Mac OS X and GNU/Linux. RAM: Problem dependent (roughly 50 bytes per grid point) Classification: 4.3, 6.5. External routines: The external libraries required are problem-dependent. Uses FFTW3 Fourier transforms (used only for FFT-based spectral methods), dSFMT random number generation (used only for stochastic problems), MPI message-passing interface (used only for distributed problems), HDF5, GNU Scientific Library (used only for Bessel-based spectral methods) and a BLAS implementation (used only for non-FFT-based spectral methods). Nature of problem: General coupled initial-value stochastic partial differential equations. Solution method: Spectral method with method-of-lines integration Running time: Determined by the size of the problem

Sub-millisecond electron density profile measurement at the JET tokamak with the fast lithium beam emission spectroscopy system

NASA Astrophysics Data System (ADS)

Réfy, D. I.; Brix, M.; Gomes, R.; Tál, B.; Zoletnik, S.; Dunai, D.; Kocsis, G.; Kálvin, S.; Szabolics, T.; JET Contributors

2018-04-01

Diagnostic alkali atom (e.g., lithium) beams are routinely used to diagnose magnetically confined plasmas, namely, to measure the plasma electron density profile in the edge and the scrape off layer region. A light splitting optics system was installed into the observation system of the lithium beam emission spectroscopy diagnostic at the Joint European Torus (JET) tokamak, which allows simultaneous measurement of the beam light emission with a spectrometer and a fast avalanche photodiode (APD) camera. The spectrometer measurement allows density profile reconstruction with ˜10 ms time resolution, absolute position calculation from the Doppler shift, spectral background subtraction as well as relative intensity calibration of the channels for each discharge. The APD system is capable of measuring light intensities on the microsecond time scale. However ˜100 μs integration is needed to have an acceptable signal to noise ratio due to moderate light levels. Fast modulation of the beam up to 30 kHz is implemented which allows background subtraction on the 100 μs time scale. The measurement covers the 0.9 < ρpol < 1.1 range with 6-10 mm optical resolution at the measurement location which translates to 3-5 mm radial resolution at the midplane due to flux expansion. An automated routine has been developed which performs the background subtraction, the relative calibration, and the comprehensive error calculation, runs a Bayesian density reconstruction code, and loads results to the JET database. The paper demonstrates the capability of the APD system by analyzing fast phenomena like pellet injection and edge localized modes.

Study of the mapping of Navier-Stokes algorithms onto multiple-instruction/multiple-data-stream computers

NASA Technical Reports Server (NTRS)

Eberhardt, D. S.; Baganoff, D.; Stevens, K.

1984-01-01

Implicit approximate-factored algorithms have certain properties that are suitable for parallel processing. A particular computational fluid dynamics (CFD) code, using this algorithm, is mapped onto a multiple-instruction/multiple-data-stream (MIMD) computer architecture. An explanation of this mapping procedure is presented, as well as some of the difficulties encountered when trying to run the code concurrently. Timing results are given for runs on the Ames Research Center's MIMD test facility which consists of two VAX 11/780's with a common MA780 multi-ported memory. Speedups exceeding 1.9 for characteristic CFD runs were indicated by the timing results.

Health Physics Code System for Evaluating Accidents Involving Radioactive Materials.

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

2014-10-01

Version 03 The HOTSPOT Health Physics codes were created to provide Health Physics personnel with a fast, field-portable calculational tool for evaluating accidents involving radioactive materials. HOTSPOT codes provide a first-order approximation of the radiation effects associated with the atmospheric release of radioactive materials. The developer's website is: http://www.llnl.gov/nhi/hotspot/. Four general programs, PLUME, EXPLOSION, FIRE, and RESUSPENSION, calculate a downwind assessment following the release of radioactive material resulting from a continuous or puff release, explosive release, fuel fire, or an area contamination event. Additional programs deal specifically with the release of plutonium, uranium, and tritium to expedite an initial assessmentmore » of accidents involving nuclear weapons. The FIDLER program can calibrate radiation survey instruments for ground survey measurements and initial screening of personnel for possible plutonium uptake in the lung. The HOTSPOT codes are fast, portable, easy to use, and fully documented in electronic help files. HOTSPOT supports color high resolution monitors and printers for concentration plots and contours. The codes have been extensively used by the DOS community since 1985. Tables and graphical output can be directed to the computer screen, printer, or a disk file. The graphical output consists of dose and ground contamination as a function of plume centerline downwind distance, and radiation dose and ground contamination contours. Users have the option of displaying scenario text on the plots. HOTSPOT 3.0.1 fixes three significant Windows 7 issues: Executable installed properly under "Program Files/HotSpot 3.0". Installation package now smaller: removed dependency on older Windows DLL files which previously needed to; Forms now properly scale based on DPI instead of font for users who change their screen resolution to something other than 100%. This is a more common feature in Windows 7; Windows installer was starting everytime most users started the program, even after HotSpot was already installed. Now, after the program is installed the installer may come up once for each new user but only the first time they run HotSpot on a particular machine. So no user should see the installer come up more than once over many uses; and GPS capability updated to directly use a serial port through a USB connection. Non-USB connections should still work. Fixed table output inconsistencies for fire scenarios.« less

CUDA Fortran acceleration for the finite-difference time-domain method

NASA Astrophysics Data System (ADS)

Hadi, Mohammed F.; Esmaeili, Seyed A.

2013-05-01

A detailed description of programming the three-dimensional finite-difference time-domain (FDTD) method to run on graphical processing units (GPUs) using CUDA Fortran is presented. Two FDTD-to-CUDA thread-block mapping designs are investigated and their performances compared. Comparative assessment of trade-offs between GPU's shared memory and L1 cache is also discussed. This presentation is for the benefit of FDTD programmers who work exclusively with Fortran and are reluctant to port their codes to C in order to utilize GPU computing. The derived CUDA Fortran code is compared with an optimized CPU version that runs on a workstation-class CPU to present a realistic GPU to CPU run time comparison and thus help in making better informed investment decisions on FDTD code redesigns and equipment upgrades. All analyses are mirrored with CUDA C simulations to put in perspective the present state of CUDA Fortran development.

DualSPHysics: A numerical tool to simulate real breakwaters

NASA Astrophysics Data System (ADS)

Zhang, Feng; Crespo, Alejandro; Altomare, Corrado; Domínguez, José; Marzeddu, Andrea; Shang, Shao-ping; Gómez-Gesteira, Moncho

2018-02-01

The open-source code DualSPHysics is used in this work to compute the wave run-up in an existing dike in the Chinese coast using realistic dimensions, bathymetry and wave conditions. The GPU computing power of the DualSPHysics allows simulating real-engineering problems that involve complex geometries with a high resolution in a reasonable computational time. The code is first validated by comparing the numerical free-surface elevation, the wave orbital velocities and the time series of the run-up with physical data in a wave flume. Those experiments include a smooth dike and an armored dike with two layers of cubic blocks. After validation, the code is applied to a real case to obtain the wave run-up under different incident wave conditions. In order to simulate the real open sea, the spurious reflections from the wavemaker are removed by using an active wave absorption technique.

Toward an automated parallel computing environment for geosciences

NASA Astrophysics Data System (ADS)

Zhang, Huai; Liu, Mian; Shi, Yaolin; Yuen, David A.; Yan, Zhenzhen; Liang, Guoping

2007-08-01

Software for geodynamic modeling has not kept up with the fast growing computing hardware and network resources. In the past decade supercomputing power has become available to most researchers in the form of affordable Beowulf clusters and other parallel computer platforms. However, to take full advantage of such computing power requires developing parallel algorithms and associated software, a task that is often too daunting for geoscience modelers whose main expertise is in geosciences. We introduce here an automated parallel computing environment built on open-source algorithms and libraries. Users interact with this computing environment by specifying the partial differential equations, solvers, and model-specific properties using an English-like modeling language in the input files. The system then automatically generates the finite element codes that can be run on distributed or shared memory parallel machines. This system is dynamic and flexible, allowing users to address different problems in geosciences. It is capable of providing web-based services, enabling users to generate source codes online. This unique feature will facilitate high-performance computing to be integrated with distributed data grids in the emerging cyber-infrastructures for geosciences. In this paper we discuss the principles of this automated modeling environment and provide examples to demonstrate its versatility.

FMM-Yukawa: An adaptive fast multipole method for screened Coulomb interactions

NASA Astrophysics Data System (ADS)

Huang, Jingfang; Jia, Jun; Zhang, Bo

2009-11-01

A Fortran program package is introduced for the rapid evaluation of the screened Coulomb interactions of N particles in three dimensions. The method utilizes an adaptive oct-tree structure, and is based on the new version of fast multipole method in which the exponential expansions are used to diagonalize the multipole-to-local translations. The program and its full description, as well as several closely related packages are also available at http://www.fastmultipole.org/. This paper is a brief review of the program and its performance. Catalogue identifier: AEEQ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEQ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPL 2.0 No. of lines in distributed program, including test data, etc.: 12 385 No. of bytes in distributed program, including test data, etc.: 79 222 Distribution format: tar.gz Programming language: Fortran77 and Fortran90 Computer: Any Operating system: Any RAM: Depends on the number of particles, their distribution, and the adaptive tree structure Classification: 4.8, 4.12 Nature of problem: To evaluate the screened Coulomb potential and force field of N charged particles, and to evaluate a convolution type integral where the Green's function is the fundamental solution of the modified Helmholtz equation. Solution method: An adaptive oct-tree is generated, and a new version of fast multipole method is applied in which the "multipole-to-local" translation operator is diagonalized. Restrictions: Only three and six significant digits accuracy options are provided in this version. Unusual features: Most of the codes are written in Fortran77. Functions for memory allocation from Fortran90 and above are used in one subroutine. Additional comments: For supplementary information see http://www.fastmultipole.org/ Running time: The running time varies depending on the number of particles (denoted by N) in the system and their distribution. The running time scales linearly as a function of N for nearly uniform particle distributions. For three digits accuracy, the solver breaks even with direct summation method at about N = 750. References: [1] L. Greengard, J. Huang, A new version of the fast multipole method for screened Coulomb interactions in three dimensions, J. Comput. Phys. 180 (2002) 642-658.

Hybrid spread spectrum radio system

DOEpatents

Smith, Stephen F.; Dress, William B.

2010-02-02

Systems and methods are described for hybrid spread spectrum radio systems. A method includes modulating a signal by utilizing a subset of bits from a pseudo-random code generator to control an amplification circuit that provides a gain to the signal. Another method includes: modulating a signal by utilizing a subset of bits from a pseudo-random code generator to control a fast hopping frequency synthesizer; and fast frequency hopping the signal with the fast hopping frequency synthesizer, wherein multiple frequency hops occur within a single data-bit time.

BALANCING THE LOAD: A VORONOI BASED SCHEME FOR PARALLEL COMPUTATIONS

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

Steinberg, Elad; Yalinewich, Almog; Sari, Re'em

2015-01-01

One of the key issues when running a simulation on multiple CPUs is maintaining a proper load balance throughout the run and minimizing communications between CPUs. We propose a novel method of utilizing a Voronoi diagram to achieve a nearly perfect load balance without the need of any global redistributions of data. As a show case, we implement our method in RICH, a two-dimensional moving mesh hydrodynamical code, but it can be extended trivially to other codes in two or three dimensions. Our tests show that this method is indeed efficient and can be used in a large variety ofmore » existing hydrodynamical codes.« less

FastChem: An ultra-fast equilibrium chemistry

NASA Astrophysics Data System (ADS)

Kitzmann, Daniel; Stock, Joachim

2018-04-01

FastChem is an equilibrium chemistry code that calculates the chemical composition of the gas phase for given temperatures and pressures. Written in C++, it is based on a semi-analytic approach, and is optimized for extremely fast and accurate calculations.

CHEETAH: A fast thermochemical code for detonation

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

Fried, L.E.

1993-11-01

For more than 20 years, TIGER has been the benchmark thermochemical code in the energetic materials community. TIGER has been widely used because it gives good detonation parameters in a very short period of time. Despite its success, TIGER is beginning to show its age. The program`s chemical equilibrium solver frequently crashes, especially when dealing with many chemical species. It often fails to find the C-J point. Finally, there are many inconveniences for the user stemming from the programs roots in pre-modern FORTRAN. These inconveniences often lead to mistakes in preparing input files and thus erroneous results. We are producingmore » a modern version of TIGER, which combines the best features of the old program with new capabilities, better computational algorithms, and improved packaging. The new code, which will evolve out of TIGER in the next few years, will be called ``CHEETAH.`` Many of the capabilities that will be put into CHEETAH are inspired by the thermochemical code CHEQ. The new capabilities of CHEETAH are: calculate trace levels of chemical compounds for environmental analysis; kinetics capability: CHEETAH will predict chemical compositions as a function of time given individual chemical reaction rates. Initial application: carbon condensation; CHEETAH will incorporate partial reactions; CHEETAH will be based on computer-optimized JCZ3 and BKW parameters. These parameters will be fit to over 20 years of data collected at LLNL. We will run CHEETAH thousands of times to determine the best possible parameter sets; CHEETAH will fit C-J data to JWL`s,and also predict full-wall and half-wall cylinder velocities.« less

Cost-effective sequencing of full-length cDNA clones powered by a de novo-reference hybrid assembly.

PubMed

Kuroshu, Reginaldo M; Watanabe, Junichi; Sugano, Sumio; Morishita, Shinichi; Suzuki, Yutaka; Kasahara, Masahiro

2010-05-07

Sequencing full-length cDNA clones is important to determine gene structures including alternative splice forms, and provides valuable resources for experimental analyses to reveal the biological functions of coded proteins. However, previous approaches for sequencing cDNA clones were expensive or time-consuming, and therefore, a fast and efficient sequencing approach was demanded. We developed a program, MuSICA 2, that assembles millions of short (36-nucleotide) reads collected from a single flow cell lane of Illumina Genome Analyzer to shotgun-sequence approximately 800 human full-length cDNA clones. MuSICA 2 performs a hybrid assembly in which an external de novo assembler is run first and the result is then improved by reference alignment of shotgun reads. We compared the MuSICA 2 assembly with 200 pooled full-length cDNA clones finished independently by the conventional primer-walking using Sanger sequencers. The exon-intron structure of the coding sequence was correct for more than 95% of the clones with coding sequence annotation when we excluded cDNA clones insufficiently represented in the shotgun library due to PCR failure (42 out of 200 clones excluded), and the nucleotide-level accuracy of coding sequences of those correct clones was over 99.99%. We also applied MuSICA 2 to full-length cDNA clones from Toxoplasma gondii, to confirm that its ability was competent even for non-human species. The entire sequencing and shotgun assembly takes less than 1 week and the consumables cost only approximately US$3 per clone, demonstrating a significant advantage over previous approaches.

Interaction between high harmonic fast waves and fast ions in NSTX/NSTX-U plasmas

NASA Astrophysics Data System (ADS)

Bertelli, N.; Valeo, E. J.; Gorelenkova, M.; Green, D. L.; RF SciDAC Team

2016-10-01

Fast wave (FW) heating in the ion cyclotron range of frequency (ICRF) has been successfully used to sustain and control the fusion plasma performance, and it will likely play an important role in the ITER experiment. As demonstrated in the NSTX and DIII-D experiments the interactions between fast waves and fast ions can be so strong to significantly modify the fast ion population from neutral beam injection. In fact, it has been recently found in NSTX that FWs can modify and, under certain conditions, even suppress the energetic particle driven instabilities, such as toroidal Alfvén eigenmodes and global Alfvén eigenmodes and fishbones. This paper examines such interactions in NSTX/NSTX-U plasmas by using the recent extension of the RF full-wave code TORIC to include non-Maxwellian ions distribution functions. Particular attention is given to the evolution of the fast ions distribution function w/ and w/o RF. Tests on the RF kick-operator implemented in the Monte-Carlo particle code NUBEAM is also discussed in order to move towards a self consistent evaluation of the RF wave-field and the ion distribution functions in the TRANSP code. Work supported by US DOE Contract DE-AC02-09CH11466.

A comparison of two types of running wheel in terms of mouse preference, health, and welfare.

PubMed

Walker, Michael; Mason, Georgia

2018-07-01

Voluntary wheel running occurs in mice of all strains, sexes, and ages. Mice find voluntary wheel running rewarding, and it leads to numerous health benefits. For this reason wheels are used both to enhance welfare and to create models of exercise. However, many designs of running wheel are used. This makes between-study comparisons difficult, as this variability could potentially affect the amount, pattern, and/or intensity of running behaviour, and thence the wheels' effects on welfare and exercise-related changes in anatomy and physiology. This study therefore evaluated two commercially available models, chosen because safe for group-housed mice: Bio Serv®'s "fast-trac" wheel combo and Ware Manufacturing Inc.'s stainless steel mesh 5″ upright wheel. Working with a total of three hundred and fifty one female C57BL/6, DBA/2 and BALB/c mice, we assessed these wheels' relative utilization by mice when access was free; the strength of motivation for each wheel-type when access required crossing an electrified grid; and the impact each wheel had on mouse well-being (inferred from acoustic startle responses and neophobia) and exercise-related anatomical changes (BMI; heart and hind limb masses). Mice ran more on the "fast-trac" wheel regardless of whether both wheel-types were available at once, or only if one was present. In terms of motivation, subjects required to work to access a single wheel worked equally hard for both wheel-types (even if locked and thus not useable for running), but if provided with one working wheel for free and the other type of wheel (again unlocked) accessible via crossing the electrified grid, the "fast-trac" wheel emerged as more motivating, as the Maximum Price Paid for the Ware metal wheel was lower than that paid for the "fast-trac" plastic wheel, at least for C57BL/6s and DBA/2s. No deleterious consequences were noted with either wheel in terms of health and welfare, but only mice with plastic wheels developed significantly larger hearts and hind limbs than control animals with locked wheels. Thus, where differences emerged, Bio Serv®'s "fast-trac" wheel combos appeared to better meet the aims of exercise provision than Ware Manufacturing's steel upright wheels. Copyright © 2018 Elsevier Inc. All rights reserved.

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

Schaumberg, Andrew

The Omics Tools package provides several small trivial tools for work in genomics. This single portable package, the “omics.jar” file, is a toolbox that works in any Java-based environment, including PCs, Macs, and supercomputers. The number of tools is expected to grow. One tool (called cmsearch.hadoop or cmsearch.local), calls the external cmsearch program to predict non-coding RNA in a genome. The cmsearch program is part of the third-party Infernal package. Omics Tools does not contain Infernal. Infernal may be installed separately. The cmsearch.hadoop subtool requires Apache Hadoop and runs on a supercomputer, though cmsearch.local does not and runs on amore » server. Omics Tools does not contain Hadoop. Hadoop mat be installed separartely The other tools (cmgbk, cmgff, fastats, pal, randgrp, randgrpr, randsub) do not interface with third-party tools. Omics Tools is written in Java and Scala programming languages. Invoking the “help” command shows currently available tools, as shown below: schaumbe@gpint06:~/proj/omics$ java -jar omics.jar help Known commands are: cmgbk : compare cmsearch and GenBank Infernal hits cmgff : compare hits among two GFF (version 3) files cmsearch.hadoop : find Infernal hits in a genome, on your supercomputer cmsearch.local : find Infernal hits in a genome, on your workstation fastats : FASTA stats, e.g. # bases, GC content pal : stem-loop motif detection by palindromic sequence search (code stub) randgrp : random subsample without replacement, of groups randgrpr : random subsample with replacement, of groups (fast) randsub : random subsample without replacement, of file lines For more help regarding a particular command, use: java -jar omics.jar command help Usage: java -jar omics.jar command args« less

Binary image encryption in a joint transform correlator scheme by aid of run-length encoding and QR code

NASA Astrophysics Data System (ADS)

Qin, Yi; Wang, Zhipeng; Wang, Hongjuan; Gong, Qiong

2018-07-01

We propose a binary image encryption method in joint transform correlator (JTC) by aid of the run-length encoding (RLE) and Quick Response (QR) code, which enables lossless retrieval of the primary image. The binary image is encoded with RLE to obtain the highly compressed data, and then the compressed binary image is further scrambled using a chaos-based method. The compressed and scrambled binary image is then transformed into one QR code that will be finally encrypted in JTC. The proposed method successfully, for the first time to our best knowledge, encodes a binary image into a QR code with the identical size of it, and therefore may probe a new way for extending the application of QR code in optical security. Moreover, the preprocessing operations, including RLE, chaos scrambling and the QR code translation, append an additional security level on JTC. We present digital results that confirm our approach.

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.

Two high-density recording methods with run-length limited turbo code for holographic data storage system

NASA Astrophysics Data System (ADS)

Nakamura, Yusuke; Hoshizawa, Taku

2016-09-01

Two methods for increasing the data capacity of a holographic data storage system (HDSS) were developed. The first method is called “run-length-limited (RLL) high-density recording”. An RLL modulation has the same effect as enlarging the pixel pitch; namely, it optically reduces the hologram size. Accordingly, the method doubles the raw-data recording density. The second method is called “RLL turbo signal processing”. The RLL turbo code consists of \\text{RLL}(1,∞ ) trellis modulation and an optimized convolutional code. The remarkable point of the developed turbo code is that it employs the RLL modulator and demodulator as parts of the error-correction process. The turbo code improves the capability of error correction more than a conventional LDPC code, even though interpixel interference is generated. These two methods will increase the data density 1.78-fold. Moreover, by simulation and experiment, a data density of 2.4 Tbit/in.2 is confirmed.

Non-Maxwellian fast particle effects in gyrokinetic GENE simulations

NASA Astrophysics Data System (ADS)

Di Siena, A.; Görler, T.; Doerk, H.; Bilato, R.; Citrin, J.; Johnson, T.; Schneider, M.; Poli, E.; JET Contributors

2018-04-01

Fast ions have recently been found to significantly impact and partially suppress plasma turbulence both in experimental and numerical studies in a number of scenarios. Understanding the underlying physics and identifying the range of their beneficial effect is an essential task for future fusion reactors, where highly energetic ions are generated through fusion reactions and external heating schemes. However, in many of the gyrokinetic codes fast ions are, for simplicity, treated as equivalent-Maxwellian-distributed particle species, although it is well known that to rigorously model highly non-thermalised particles, a non-Maxwellian background distribution function is needed. To study the impact of this assumption, the gyrokinetic code GENE has recently been extended to support arbitrary background distribution functions which might be either analytical, e.g., slowing down and bi-Maxwellian, or obtained from numerical fast ion models. A particular JET plasma with strong fast-ion related turbulence suppression is revised with these new code capabilities both with linear and nonlinear gyrokinetic simulations. It appears that the fast ion stabilization tends to be less strong but still substantial with more realistic distributions, and this improves the quantitative power balance agreement with experiments.

Comparing Effects of Feedstock and Run Conditions on Pyrolysis Products Produced at Pilot-Scale

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

Dunning, Timothy C; Gaston, Katherine R; Wilcox, Esther

2018-01-19

Fast pyrolysis is a promising pathway for mass production of liquid transportable biofuels. The Thermochemical Process Development Unit (TCPDU) pilot plant at NREL is conducting research to support the Bioenergy Technologies Office's 2017 goal of a $3 per gallon biofuel. In preparation for down select of feedstock and run conditions, four different feedstocks were run at three different run conditions. The products produced were characterized extensively. Hot pyrolysis vapors and light gasses were analyzed on a slip stream, and oil and char samples were characterized post run.

Efficient image compression algorithm for computer-animated images

NASA Astrophysics Data System (ADS)

Yfantis, Evangelos A.; Au, Matthew Y.; Miel, G.

1992-10-01

An image compression algorithm is described. The algorithm is an extension of the run-length image compression algorithm and its implementation is relatively easy. This algorithm was implemented and compared with other existing popular compression algorithms and with the Lempel-Ziv (LZ) coding. The Lempel-Ziv algorithm is available as a utility in the UNIX operating system and is also referred to as the UNIX uncompress. Sometimes our algorithm is best in terms of saving memory space, and sometimes one of the competing algorithms is best. The algorithm is lossless, and the intent is for the algorithm to be used in computer graphics animated images. Comparisons made with the LZ algorithm indicate that the decompression time using our algorithm is faster than that using the LZ algorithm. Once the data are in memory, a relatively simple and fast transformation is applied to uncompress the file.

SWIFT: SPH With Inter-dependent Fine-grained Tasking

NASA Astrophysics Data System (ADS)

Schaller, Matthieu; Gonnet, Pedro; Chalk, Aidan B. G.; Draper, Peter W.

2018-05-01

SWIFT runs cosmological simulations on peta-scale machines for solving gravity and SPH. It uses the Fast Multipole Method (FMM) to calculate gravitational forces between nearby particles, combining these with long-range forces provided by a mesh that captures both the periodic nature of the calculation and the expansion of the simulated universe. SWIFT currently uses a single fixed but time-variable softening length for all the particles. Many useful external potentials are also available, such as galaxy haloes or stratified boxes that are used in idealised problems. SWIFT implements a standard LCDM cosmology background expansion and solves the equations in a comoving frame; equations of state of dark-energy evolve with scale-factor. The structure of the code allows implementation for modified-gravity solvers or self-interacting dark matter schemes to be implemented. Many hydrodynamics schemes are implemented in SWIFT and the software allows users to add their own.

The Effects of Treadmill Running on Aging Laryngeal Muscle Structure

PubMed Central

Kletzien, Heidi; Russell, John A.; Connor, Nadine P.

2015-01-01

Levels of Evidence NA (animal study) Objective Age-related changes in laryngeal muscle structure and function may contribute to deficits in voice and swallowing observed in elderly people. We hypothesized that treadmill running, an exercise that increases respiratory drive to upper airway muscles, would induce changes in thyroarytenoid muscle myosin heavy chain (MHC) isoforms consistent with a fast-slow transformation in muscle fiber type. Study Design Randomized parallel group controlled trial. Methods Fifteen young adult and 14 old Fischer 344/Brown Norway rats received either treadmill running or no exercise (5 days/week/8 weeks). Myosin heavy chain isoform composition in the thyroarytenoid muscle was examined at the end of 8 weeks. Results Significant age and treatment effects were found. The young adult group had the greatest proportion of superfast contracting MHCIIL. The treadmill running group had the lowest proportion of MHCIIL and the greatest proportion of MHCIIx. Conclusion Thyroarytenoid muscle structure was affected both by age and treadmill running in a fast-slow transition that is characteristic of exercise manipulations in other skeletal muscles. PMID:26256100

Inter-view prediction of intra mode decision for high-efficiency video coding-based multiview video coding

NASA Astrophysics Data System (ADS)

da Silva, Thaísa Leal; Agostini, Luciano Volcan; da Silva Cruz, Luis A.

2014-05-01

Intra prediction is a very important tool in current video coding standards. High-efficiency video coding (HEVC) intra prediction presents relevant gains in encoding efficiency when compared to previous standards, but with a very important increase in the computational complexity since 33 directional angular modes must be evaluated. Motivated by this high complexity, this article presents a complexity reduction algorithm developed to reduce the HEVC intra mode decision complexity targeting multiview videos. The proposed algorithm presents an efficient fast intra prediction compliant with singleview and multiview video encoding. This fast solution defines a reduced subset of intra directions according to the video texture and it exploits the relationship between prediction units (PUs) of neighbor depth levels of the coding tree. This fast intra coding procedure is used to develop an inter-view prediction method, which exploits the relationship between the intra mode directions of adjacent views to further accelerate the intra prediction process in multiview video encoding applications. When compared to HEVC simulcast, our method achieves a complexity reduction of up to 47.77%, at the cost of an average BD-PSNR loss of 0.08 dB.

Fast QC-LDPC code for free space optical communication

NASA Astrophysics Data System (ADS)

Wang, Jin; Zhang, Qi; Udeh, Chinonso Paschal; Wu, Rangzhong

2017-02-01

Free Space Optical (FSO) Communication systems use the atmosphere as a propagation medium. Hence the atmospheric turbulence effects lead to multiplicative noise related with signal intensity. In order to suppress the signal fading induced by multiplicative noise, we propose a fast Quasi-Cyclic (QC) Low-Density Parity-Check (LDPC) code for FSO Communication systems. As a linear block code based on sparse matrix, the performances of QC-LDPC is extremely near to the Shannon limit. Currently, the studies on LDPC code in FSO Communications is mainly focused on Gauss-channel and Rayleigh-channel, respectively. In this study, the LDPC code design over atmospheric turbulence channel which is nether Gauss-channel nor Rayleigh-channel is closer to the practical situation. Based on the characteristics of atmospheric channel, which is modeled as logarithmic-normal distribution and K-distribution, we designed a special QC-LDPC code, and deduced the log-likelihood ratio (LLR). An irregular QC-LDPC code for fast coding, of which the rates are variable, is proposed in this paper. The proposed code achieves excellent performance of LDPC codes and can present the characteristics of high efficiency in low rate, stable in high rate and less number of iteration. The result of belief propagation (BP) decoding shows that the bit error rate (BER) obviously reduced as the Signal-to-Noise Ratio (SNR) increased. Therefore, the LDPC channel coding technology can effectively improve the performance of FSO. At the same time, the BER, after decoding reduces with the increase of SNR arbitrarily, and not having error limitation platform phenomenon with error rate slowing down.

Coding for reliable satellite communications

NASA Technical Reports Server (NTRS)

Lin, S.

1984-01-01

Several error control coding techniques for reliable satellite communications were investigated to find algorithms for fast decoding of Reed-Solomon codes in terms of dual basis. The decoding of the (255,223) Reed-Solomon code, which is used as the outer code in the concatenated TDRSS decoder, was of particular concern.

Particle-gas dynamics in the protoplanetary nebula

NASA Technical Reports Server (NTRS)

Cuzzi, Jeffrey N.; Champney, Joelle M.; Dobrovolskis, Anthony R.

1991-01-01

In the past year we made significant progress in improving our fundamental understanding of the physics of particle-gas dynamics in the protoplanetary nebula. Having brought our code to a state of fairly robust functionality, we devoted significant effort to optimizing it for running long cases. We optimized the code for vectorization to the extent that it now runs eight times faster than before. The following subject areas are covered: physical improvements to the model; numerical results; Reynolds averaging of fluid equations; and modeling of turbulence and viscosity.

Adaptive Integration of Nonsmooth Dynamical Systems

DTIC Science & Technology

2017-10-11

controlled time stepping method to interactively design running robots. [1] John Shepherd, Samuel Zapolsky, and Evan M. Drumwright, “Fast multi-body...software like this to test software running on my robots. Started working in simulation after attempting to use software like this to test software... running on my robots. The libraries that produce these beautiful results have failed at simulating robotic manipulation. Postulate: It is easier to

Epoch of Reionization : An Investigation of the Semi-Analytic 21CMMC Code

NASA Astrophysics Data System (ADS)

Miller, Michelle

2018-01-01

After the Big Bang the universe was filled with neutral hydrogen that began to cool and collapse into the first structures. These first stars and galaxies began to emit radiation that eventually ionized all of the neutral hydrogen in the universe. 21CMMC is a semi-numerical code that takes simulated boxes of this ionized universe from another code called 21cmFAST. Mock measurements are taken from the simulated boxes in 21cmFAST. Those measurements are thrown into 21CMMC and help us determine three major parameters of this simulated universe: virial temperature, mean free path, and ionization efficiency. My project tests the robustness of 21CMMC on universe simulations other than 21cmFAST to see whether 21CMMC can properly reconstruct early universe parameters given a mock “measurement” in the form of power spectra. We determine that while two of the three EoR parameters (Virial Temperature and Efficiency) have some reconstructability, the mean free path parameter in the code is the least robust. This requires development of the 21CMMC code.

Proceedings of the Interservice/Industry Training Systems Conference (9th), Held at Washington, DC, on 30 November - 2 December 1987

DTIC Science & Technology

1987-12-01

requires much more data, but holds fast to the idea that the FV approach, or some other model, is critical if the job analysis process is to have its...Ada compiled code executes twice as fast as Microsoft’s Fortran compiled code. This conclusion is at variance with the results obtained from...finish is not so important. Hence, if a design methodology produces coda that will not execute fast enough on processors suitable for flight

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 .

Improving fast generation of halo catalogues with higher order Lagrangian perturbation theory

NASA Astrophysics Data System (ADS)

Munari, Emiliano; Monaco, Pierluigi; Sefusatti, Emiliano; Castorina, Emanuele; Mohammad, Faizan G.; Anselmi, Stefano; Borgani, Stefano

2017-03-01

We present the latest version of PINOCCHIO, a code that generates catalogues of dark matter haloes in an approximate but fast way with respect to an N-body simulation. This code version implements a new on-the-fly production of halo catalogue on the past light cone with continuous time sampling, and the computation of particle and halo displacements are extended up to third-order Lagrangian perturbation theory (LPT), in contrast with previous versions that used Zel'dovich approximation. We run PINOCCHIO on the same initial configuration of a reference N-body simulation, so that the comparison extends to the object-by-object level. We consider haloes at redshifts 0 and 1, using different LPT orders either for halo construction or to compute halo final positions. We compare the clustering properties of PINOCCHIO haloes with those from the simulation by computing the power spectrum and two-point correlation function in real and redshift space (monopole and quadrupole), the bispectrum and the phase difference of halo distributions. We find that 2LPT and 3LPT give noticeable improvement. 3LPT provides the best agreement with N-body when it is used to displace haloes, while 2LPT gives better results for constructing haloes. At the highest orders, linear bias is typically recovered at a few per cent level. In Fourier space and using 3LPT for halo displacements, the halo power spectrum is recovered to within 10 per cent up to kmax ∼ 0.5 h Mpc-1. The results presented in this paper have interesting implications for the generation of large ensemble of mock surveys for the scientific exploitation of data from big surveys.

Follow the Code: Rules or Guidelines for Academic Deans' Behavior?

ERIC Educational Resources Information Center

Bray, Nathaniel J.

2012-01-01

In the popular movie series "Pirates of the Caribbean," there is a pirate code that influences how pirates behave in unclear situations, with a running joke about whether the code is either a set of rules or guidelines for behavior. Codes of conduct in any social group or organization can have much the same feel; they can provide clarity and…

Calculation and benchmarking of an azimuthal pressure vessel neutron fluence distribution using the BOXER code and scraping experiments

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

Holzgrewe, F.; Hegedues, F.; Paratte, J.M.

1995-03-01

The light water reactor BOXER code was used to determine the fast azimuthal neutron fluence distribution at the inner surface of the reactor pressure vessel after the tenth cycle of a pressurized water reactor (PWR). Using a cross-section library in 45 groups, fixed-source calculations in transport theory and x-y geometry were carried out to determine the fast azimuthal neutron flux distribution at the inner surface of the pressure vessel for four different cycles. From these results, the fast azimuthal neutron fluence after the tenth cycle was estimated and compared with the results obtained from scraping test experiments. In these experiments,more » small samples of material were taken from the inner surface of the pressure vessel. The fast neutron fluence was then determined form the measured activity of the samples. Comparing the BOXER and scraping test results have maximal differences of 15%, which is very good, considering the factor of 10{sup 3} neutron attenuation between the reactor core and the pressure vessel. To compare the BOXER results with an independent code, the 21st cycle of the PWR was also calculated with the TWODANT two-dimensional transport code, using the same group structure and cross-section library. Deviations in the fast azimuthal flux distribution were found to be <3%, which verifies the accuracy of the BOXER results.« less

Experiences with Cray multi-tasking

NASA Technical Reports Server (NTRS)

Miya, E. N.

1985-01-01

The issues involved in modifying an existing code for multitasking is explored. They include Cray extensions to FORTRAN, an examination of the application code under study, designing workable modifications, specific code modifications to the VAX and Cray versions, performance, and efficiency results. The finished product is a faster, fully synchronous, parallel version of the original program. A production program is partitioned by hand to run on two CPUs. Loop splitting multitasks three key subroutines. Simply dividing subroutine data and control structure down the middle of a subroutine is not safe. Simple division produces results that are inconsistent with uniprocessor runs. The safest way to partition the code is to transfer one block of loops at a time and check the results of each on a test case. Other issues include debugging and performance. Task startup and maintenance (e.g., synchronization) are potentially expensive.

NASA One-Dimensional Combustor Simulation--User Manual for S1D_ML

NASA Technical Reports Server (NTRS)

Stueber, Thomas J.; Paxson, Daniel E.

2014-01-01

The work presented in this paper is to promote research leading to a closed-loop control system to actively suppress thermo-acoustic instabilities. To serve as a model for such a closed-loop control system, a one-dimensional combustor simulation composed using MATLAB software tools has been written. This MATLAB based process is similar to a precursor one-dimensional combustor simulation that was formatted as FORTRAN 77 source code. The previous simulation process requires modification to the FORTRAN 77 source code, compiling, and linking when creating a new combustor simulation executable file. The MATLAB based simulation does not require making changes to the source code, recompiling, or linking. Furthermore, the MATLAB based simulation can be run from script files within the MATLAB environment or with a compiled copy of the executable file running in the Command Prompt window without requiring a licensed copy of MATLAB. This report presents a general simulation overview. Details regarding how to setup and initiate a simulation are also presented. Finally, the post-processing section describes the two types of files created while running the simulation and it also includes simulation results for a default simulation included with the source code.

CBP Toolbox Version 3.0 “Beta Testing” Performance Evaluation

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

Smith, III, F. G.

2016-07-29

One function of the Cementitious Barriers Partnership (CBP) is to assess available models of cement degradation and to assemble suitable models into a “Toolbox” that would be made available to members of the partnership, as well as the DOE Complex. To this end, SRNL and Vanderbilt University collaborated to develop an interface using the GoldSim software to the STADIUM @ code developed by SIMCO Technologies, Inc. and LeachXS/ORCHESTRA developed by Energy research Centre of the Netherlands (ECN). Release of Version 3.0 of the CBP Toolbox is planned in the near future. As a part of this release, an increased levelmore » of quality assurance for the partner codes and the GoldSim interface has been developed. This report documents results from evaluation testing of the ability of CBP Toolbox 3.0 to perform simulations of concrete degradation applicable to performance assessment of waste disposal facilities. Simulations of the behavior of Savannah River Saltstone Vault 2 and Vault 1/4 concrete subject to sulfate attack and carbonation over a 500- to 1000-year time period were run using a new and upgraded version of the STADIUM @ code and the version of LeachXS/ORCHESTRA released in Version 2.0 of the CBP Toolbox. Running both codes allowed comparison of results from two models which take very different approaches to simulating cement degradation. In addition, simulations of chloride attack on the two concretes were made using the STADIUM @ code. The evaluation sought to demonstrate that: 1) the codes are capable of running extended realistic simulations in a reasonable amount of time; 2) the codes produce “reasonable” results; the code developers have provided validation test results as part of their code QA documentation; and 3) the two codes produce results that are consistent with one another. Results of the evaluation testing showed that the three criteria listed above were met by the CBP partner codes. Therefore, it is concluded that the codes can be used to support performance assessment. This conclusion takes into account the QA documentation produced for the partner codes and for the CBP Toolbox.« less

FAST-PT: a novel algorithm to calculate convolution integrals in cosmological perturbation theory

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

McEwen, Joseph E.; Fang, Xiao; Hirata, Christopher M.

2016-09-01

We present a novel algorithm, FAST-PT, for performing convolution or mode-coupling integrals that appear in nonlinear cosmological perturbation theory. The algorithm uses several properties of gravitational structure formation—the locality of the dark matter equations and the scale invariance of the problem—as well as Fast Fourier Transforms to describe the input power spectrum as a superposition of power laws. This yields extremely fast performance, enabling mode-coupling integral computations fast enough to embed in Monte Carlo Markov Chain parameter estimation. We describe the algorithm and demonstrate its application to calculating nonlinear corrections to the matter power spectrum, including one-loop standard perturbation theorymore » and the renormalization group approach. We also describe our public code (in Python) to implement this algorithm. The code, along with a user manual and example implementations, is available at https://github.com/JoeMcEwen/FAST-PT.« less

Review of Hybrid (Deterministic/Monte Carlo) Radiation Transport Methods, Codes, and Applications at Oak Ridge National Laboratory

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

Wagner, John C; Peplow, Douglas E.; Mosher, Scott W

2010-01-01

This paper provides a review of the hybrid (Monte Carlo/deterministic) radiation transport methods and codes used at the Oak Ridge National Laboratory and examples of their application for increasing the efficiency of real-world, fixed-source Monte Carlo analyses. The two principal hybrid methods are (1) Consistent Adjoint Driven Importance Sampling (CADIS) for optimization of a localized detector (tally) region (e.g., flux, dose, or reaction rate at a particular location) and (2) Forward Weighted CADIS (FW-CADIS) for optimizing distributions (e.g., mesh tallies over all or part of the problem space) or multiple localized detector regions (e.g., simultaneous optimization of two or moremore » localized tally regions). The two methods have been implemented and automated in both the MAVRIC sequence of SCALE 6 and ADVANTG, a code that works with the MCNP code. As implemented, the methods utilize the results of approximate, fast-running 3-D discrete ordinates transport calculations (with the Denovo code) to generate consistent space- and energy-dependent source and transport (weight windows) biasing parameters. These methods and codes have been applied to many relevant and challenging problems, including calculations of PWR ex-core thermal detector response, dose rates throughout an entire PWR facility, site boundary dose from arrays of commercial spent fuel storage casks, radiation fields for criticality accident alarm system placement, and detector response for special nuclear material detection scenarios and nuclear well-logging tools. Substantial computational speed-ups, generally O(10{sup 2-4}), have been realized for all applications to date. This paper provides a brief review of the methods, their implementation, results of their application, and current development activities, as well as a considerable list of references for readers seeking more information about the methods and/or their applications.« less

Automated JPSS VIIRS GEO code change testing by using Chain Run Scripts

NASA Astrophysics Data System (ADS)

Chen, W.; Wang, W.; Zhao, Q.; Das, B.; Mikles, V. J.; Sprietzer, K.; Tsidulko, M.; Zhao, Y.; Dharmawardane, V.; Wolf, W.

2015-12-01

The Joint Polar Satellite System (JPSS) is the next generation polar-orbiting operational environmental satellite system. The first satellite in the JPSS series of satellites, J-1, is scheduled to launch in early 2017. J1 will carry similar versions of the instruments that are on board of Suomi National Polar-Orbiting Partnership (S-NPP) satellite which was launched on October 28, 2011. The center for Satellite Applications and Research Algorithm Integration Team (STAR AIT) uses the Algorithm Development Library (ADL) to run S-NPP and pre-J1 algorithms in a development and test mode. The ADL is an offline test system developed by Raytheon to mimic the operational system while enabling a development environment for plug and play algorithms. The Perl Chain Run Scripts have been developed by STAR AIT to automate the staging and processing of multiple JPSS Sensor Data Record (SDR) and Environmental Data Record (EDR) products. JPSS J1 VIIRS Day Night Band (DNB) has anomalous non-linear response at high scan angles based on prelaunch testing. The flight project has proposed multiple mitigation options through onboard aggregation, and the Option 21 has been suggested by the VIIRS SDR team as the baseline aggregation mode. VIIRS GEOlocation (GEO) code analysis results show that J1 DNB GEO product cannot be generated correctly without the software update. The modified code will support both Op21, Op21/26 and is backward compatible with SNPP. J1 GEO code change version 0 delivery package is under development for the current change request. In this presentation, we will discuss how to use the Chain Run Script to verify the code change and Lookup Tables (LUTs) update in ADL Block2.

Active Acoustics using Bellhop-DRDC: Run Time Tests and Suggested Configurations for a Tracking Exercise in Shallow Scotian Waters

DTIC Science & Technology

2005-05-01

simulée d’essai pour obtenir les diagrammes de perte de transmission et de réverbération pour 18 éléments (une source, un réseau remorqué et 16 bouées...were recorded using a 1.5GHz Pentium 4 processor. The test results indicate that the Bellhop program runs fast enough to provide the required acoustic...was determined that the Bellhop program will be fast enough for these clients. Future Plans It is intended to integrate further enhancements that

ENDF/B-VII.0 Data Testing Using 1,172 Critical Assemblies

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

Plechaty, E F; Cullen, D E

2007-10-01

In order to test the ENDF/B-VII.0 neutron data library [1], 1,172 critical assemblies from [2] have been calculated using the Monte Carlo transport code TART [3]. TART's 'best' physics was used for all of these calculations; this included continuous energy cross sections, delayed neutrons in their spectrum that is slower than prompt neutrons, unresolved resonance region self-shielding, the thermal scattering (free atom for all materials plus thermal scattering law data S({alpha},{beta}) when available). In this first pass through the assemblies the objective was to 'quickly' test the validity of the ENDF/B-VII.0 data [1], the assembly models as defined in [2]more » and coded for use with TART, and TART's physics treatment [3] of these assemblies. With TART we have the option of running criticality problems until K-eff has been calculated to an acceptable input accuracy. In order to 'quickly' calculate all of these assemblies K-eff was calculated in each case to +/- 0.002. For these calculations the assemblies were divided into ten types based on fuel (mixed, Pu239, U233, U235) and median fission energy (Fast, Midi, Slow). A table is provided that shows a summary of these results. This is followed be details for every assembly, and statistical information about the distribution of K-eff for each type of assembly. After a review of these results to eliminate any obvious errors in ENDF/B data, assembly models, or TART physics, all assemblies will be run again to a higher precision. Only after this second run is finished will we have highly precise results. Until then the results presently here should only be interpreted as approximate values of K-eff with a standard deviation of +/- 0.002; for such a large number of assemblies we expected the results to be approximately normal, with a spread out to several times the standard deviation; see the calculated statistical distributions and their comparisons to a normal distribution.« less

NLSEmagic: Nonlinear Schrödinger equation multi-dimensional Matlab-based GPU-accelerated integrators using compact high-order schemes

NASA Astrophysics Data System (ADS)

Caplan, R. M.

2013-04-01

We present a simple to use, yet powerful code package called NLSEmagic to numerically integrate the nonlinear Schrödinger equation in one, two, and three dimensions. NLSEmagic is a high-order finite-difference code package which utilizes graphic processing unit (GPU) parallel architectures. The codes running on the GPU are many times faster than their serial counterparts, and are much cheaper to run than on standard parallel clusters. The codes are developed with usability and portability in mind, and therefore are written to interface with MATLAB utilizing custom GPU-enabled C codes with the MEX-compiler interface. The packages are freely distributed, including user manuals and set-up files. Catalogue identifier: AEOJ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEOJ_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 124453 No. of bytes in distributed program, including test data, etc.: 4728604 Distribution format: tar.gz Programming language: C, CUDA, MATLAB. Computer: PC, MAC. Operating system: Windows, MacOS, Linux. Has the code been vectorized or parallelized?: Yes. Number of processors used: Single CPU, number of GPU processors dependent on chosen GPU card (max is currently 3072 cores on GeForce GTX 690). Supplementary material: Setup guide, Installation guide. RAM: Highly dependent on dimensionality and grid size. For typical medium-large problem size in three dimensions, 4GB is sufficient. Keywords: Nonlinear Schröodinger Equation, GPU, high-order finite difference, Bose-Einstien condensates. Classification: 4.3, 7.7. Nature of problem: Integrate solutions of the time-dependent one-, two-, and three-dimensional cubic nonlinear Schrödinger equation. Solution method: The integrators utilize a fully-explicit fourth-order Runge-Kutta scheme in time and both second- and fourth-order differencing in space. The integrators are written to run on NVIDIA GPUs and are interfaced with MATLAB including built-in visualization and analysis tools. Restrictions: The main restriction for the GPU integrators is the amount of RAM on the GPU as the code is currently only designed for running on a single GPU. Unusual features: Ability to visualize real-time simulations through the interaction of MATLAB and the compiled GPU integrators. Additional comments: Setup guide and Installation guide provided. Program has a dedicated web site at www.nlsemagic.com. Running time: A three-dimensional run with a grid dimension of 87×87×203 for 3360 time steps (100 non-dimensional time units) takes about one and a half minutes on a GeForce GTX 580 GPU card.

Proximity of fast food restaurants to schools: do neighborhood income and type of school matter?

PubMed

Simon, Paul A; Kwan, David; Angelescu, Aida; Shih, Margaret; Fielding, Jonathan E

2008-09-01

To investigate the proximity of fast food restaurants to public schools and examine proximity by neighborhood income and school level (elementary, middle, or high school). Geocoded school and restaurant databases from 2005 and 2003, respectively, were used to determine the percentage of schools with one or more fast food restaurants within 400 m and 800 m of all public schools in Los Angeles County, California. Single-factor analysis of variance (ANOVA) models were run to examine fast food restaurant proximity to schools by median household income of the surrounding census tract and by school level. Two-factor ANOVA models were run to assess the additional influence of neighborhood level of commercialization. Overall, 23.3% and 64.8% of schools had one or more fast food restaurants located within 400 m and 800 m, respectively. Fast food restaurant proximity was greater for high schools than for middle and elementary schools, and was inversely related to neighborhood income for schools in the highest commercial areas. No association with income was observed in less commercial areas. Fast food restaurants are located in close proximity to many schools in this large metropolitan area, especially high schools and schools located in low income highly commercial neighborhoods. Further research is needed to assess the relationship between fast food proximity and student dietary practices and obesity risk.

VizieR Online Data Catalog: ynogkm: code for calculating time-like geodesics (Yang+, 2014)

NASA Astrophysics Data System (ADS)

Yang, X.-L.; Wang, J.-C.

2013-11-01

Here we present the source file for a new public code named ynogkm, aim on calculating the time-like geodesics in a Kerr-Newmann spacetime fast. In the code the four Boyer-Lindquis coordinates and proper time are expressed as functions of a parameter p semi-analytically, i.e., r(p), μ(p), φ(p), t(p), and σ(p), by using the Weiers- trass' and Jacobi's elliptic functions and integrals. All of the ellip- tic integrals are computed by Carlson's elliptic integral method, which guarantees the fast speed of the code.The source Fortran file ynogkm.f90 contains three modules: constants, rootfind, ellfunction, and blcoordinates. (3 data files).

2D-pattern matching image and video compression: theory, algorithms, and experiments.

PubMed

Alzina, Marc; Szpankowski, Wojciech; Grama, Ananth

2002-01-01

In this paper, we propose a lossy data compression framework based on an approximate two-dimensional (2D) pattern matching (2D-PMC) extension of the Lempel-Ziv (1977, 1978) lossless scheme. This framework forms the basis upon which higher level schemes relying on differential coding, frequency domain techniques, prediction, and other methods can be built. We apply our pattern matching framework to image and video compression and report on theoretical and experimental results. Theoretically, we show that the fixed database model used for video compression leads to suboptimal but computationally efficient performance. The compression ratio of this model is shown to tend to the generalized entropy. For image compression, we use a growing database model for which we provide an approximate analysis. The implementation of 2D-PMC is a challenging problem from the algorithmic point of view. We use a range of techniques and data structures such as k-d trees, generalized run length coding, adaptive arithmetic coding, and variable and adaptive maximum distortion level to achieve good compression ratios at high compression speeds. We demonstrate bit rates in the range of 0.25-0.5 bpp for high-quality images and data rates in the range of 0.15-0.5 Mbps for a baseline video compression scheme that does not use any prediction or interpolation. We also demonstrate that this asymmetric compression scheme is capable of extremely fast decompression making it particularly suitable for networked multimedia applications.

The Five 'R's' for Developing Trusted Software Frameworks to increase confidence in, and maximise reuse of, Open Source Software.

NASA Astrophysics Data System (ADS)

Fraser, Ryan; Gross, Lutz; Wyborn, Lesley; Evans, Ben; Klump, Jens

2015-04-01

Recent investments in HPC, cloud and Petascale data stores, have dramatically increased the scale and resolution that earth science challenges can now be tackled. These new infrastructures are highly parallelised and to fully utilise them and access the large volumes of earth science data now available, a new approach to software stack engineering needs to be developed. The size, complexity and cost of the new infrastructures mean any software deployed has to be reliable, trusted and reusable. Increasingly software is available via open source repositories, but these usually only enable code to be discovered and downloaded. As a user it is hard for a scientist to judge the suitability and quality of individual codes: rarely is there information on how and where codes can be run, what the critical dependencies are, and in particular, on the version requirements and licensing of the underlying software stack. A trusted software framework is proposed to enable reliable software to be discovered, accessed and then deployed on multiple hardware environments. More specifically, this framework will enable those who generate the software, and those who fund the development of software, to gain credit for the effort, IP, time and dollars spent, and facilitate quantification of the impact of individual codes. For scientific users, the framework delivers reviewed and benchmarked scientific software with mechanisms to reproduce results. The trusted framework will have five separate, but connected components: Register, Review, Reference, Run, and Repeat. 1) The Register component will facilitate discovery of relevant software from multiple open source code repositories. The registration process of the code should include information about licensing, hardware environments it can be run on, define appropriate validation (testing) procedures and list the critical dependencies. 2) The Review component is targeting on the verification of the software typically against a set of benchmark cases. This will be achieved by linking the code in the software framework to peer review forums such as Mozilla Science or appropriate Journals (e.g. Geoscientific Model Development Journal) to assist users to know which codes to trust. 3) Referencing will be accomplished by linking the Software Framework to groups such as Figshare or ImpactStory that help disseminate and measure the impact of scientific research, including program code. 4) The Run component will draw on information supplied in the registration process, benchmark cases described in the review and relevant information to instantiate the scientific code on the selected environment. 5) The Repeat component will tap into existing Provenance Workflow engines that will automatically capture information that relate to a particular run of that software, including identification of all input and output artefacts, and all elements and transactions within that workflow. The proposed trusted software framework will enable users to rapidly discover and access reliable code, reduce the time to deploy it and greatly facilitate sharing, reuse and reinstallation of code. Properly designed it could enable an ability to scale out to massively parallel systems and be accessed nationally/ internationally for multiple use cases, including Supercomputer centres, cloud facilities, and local computers.

AFMPB: An adaptive fast multipole Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems

NASA Astrophysics Data System (ADS)

Lu, Benzhuo; Cheng, Xiaolin; Huang, Jingfang; McCammon, J. Andrew

2010-06-01

A Fortran program package is introduced for rapid evaluation of the electrostatic potentials and forces in biomolecular systems modeled by the linearized Poisson-Boltzmann equation. The numerical solver utilizes a well-conditioned boundary integral equation (BIE) formulation, a node-patch discretization scheme, a Krylov subspace iterative solver package with reverse communication protocols, and an adaptive new version of fast multipole method in which the exponential expansions are used to diagonalize the multipole-to-local translations. The program and its full description, as well as several closely related libraries and utility tools are available at http://lsec.cc.ac.cn/~lubz/afmpb.html and a mirror site at http://mccammon.ucsd.edu/. This paper is a brief summary of the program: the algorithms, the implementation and the usage. Program summaryProgram title: AFMPB: Adaptive fast multipole Poisson-Boltzmann solver Catalogue identifier: AEGB_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGB_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPL 2.0 No. of lines in distributed program, including test data, etc.: 453 649 No. of bytes in distributed program, including test data, etc.: 8 764 754 Distribution format: tar.gz Programming language: Fortran Computer: Any Operating system: Any RAM: Depends on the size of the discretized biomolecular system Classification: 3 External routines: Pre- and post-processing tools are required for generating the boundary elements and for visualization. Users can use MSMS ( http://www.scripps.edu/~sanner/html/msms_home.html) for pre-processing, and VMD ( http://www.ks.uiuc.edu/Research/vmd/) for visualization. Sub-programs included: An iterative Krylov subspace solvers package from SPARSKIT by Yousef Saad ( http://www-users.cs.umn.edu/~saad/software/SPARSKIT/sparskit.html), and the fast multipole methods subroutines from FMMSuite ( http://www.fastmultipole.org/). Nature of problem: Numerical solution of the linearized Poisson-Boltzmann equation that describes electrostatic interactions of molecular systems in ionic solutions. Solution method: A novel node-patch scheme is used to discretize the well-conditioned boundary integral equation formulation of the linearized Poisson-Boltzmann equation. Various Krylov subspace solvers can be subsequently applied to solve the resulting linear system, with a bounded number of iterations independent of the number of discretized unknowns. The matrix-vector multiplication at each iteration is accelerated by the adaptive new versions of fast multipole methods. The AFMPB solver requires other stand-alone pre-processing tools for boundary mesh generation, post-processing tools for data analysis and visualization, and can be conveniently coupled with different time stepping methods for dynamics simulation. Restrictions: Only three or six significant digits options are provided in this version. Unusual features: Most of the codes are in Fortran77 style. Memory allocation functions from Fortran90 and above are used in a few subroutines. Additional comments: The current version of the codes is designed and written for single core/processor desktop machines. Check http://lsec.cc.ac.cn/~lubz/afmpb.html and http://mccammon.ucsd.edu/ for updates and changes. Running time: The running time varies with the number of discretized elements ( N) in the system and their distributions. In most cases, it scales linearly as a function of N.

CAFNA{reg{underscore}sign}, coded aperture fast neutron analysis for contraband detection: Preliminary results

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

Zhang, L.; Lanza, R.C.

1999-12-01

The authors have developed a near field coded aperture imaging system for use with fast neutron techniques as a tool for the detection of contraband and hidden explosives through nuclear elemental analysis. The technique relies on the prompt gamma rays produced by fast neutron interactions with the object being examined. The position of the nuclear elements is determined by the location of the gamma emitters. For existing fast neutron techniques, in Pulsed Fast Neutron Analysis (PFNA), neutrons are used with very low efficiency; in Fast Neutron Analysis (FNS), the sensitivity for detection of the signature gamma rays is very low.more » For the Coded Aperture Fast Neutron Analysis (CAFNA{reg{underscore}sign}) the authors have developed, the efficiency for both using the probing fast neutrons and detecting the prompt gamma rays is high. For a probed volume of n{sup 3} volume elements (voxels) in a cube of n resolution elements on a side, they can compare the sensitivity with other neutron probing techniques. As compared to PFNA, the improvement for neutron utilization is n{sup 2}, where the total number of voxels in the object being examined is n{sup 3}. Compared to FNA, the improvement for gamma-ray imaging is proportional to the total open area of the coded aperture plane; a typical value is n{sup 2}/2, where n{sup 2} is the number of total detector resolution elements or the number of pixels in an object layer. It should be noted that the actual signal to noise ratio of a system depends also on the nature and distribution of background events and this comparison may reduce somewhat the effective sensitivity of CAFNA. They have performed analysis, Monte Carlo simulations, and preliminary experiments using low and high energy gamma-ray sources. The results show that a high sensitivity 3-D contraband imaging and detection system can be realized by using CAFNA.« less

Redistribution of Mechanical Work at the Knee and Ankle Joints During Fast Running in Minimalist Shoes.

PubMed

Fuller, Joel T; Buckley, Jonathan D; Tsiros, Margarita D; Brown, Nicholas A T; Thewlis, Dominic

2016-10-01

Minimalist shoes have been suggested as a way to alter running biomechanics to improve running performance and reduce injuries. However, to date, researchers have only considered the effect of minimalist shoes at slow running speeds. To determine if runners change foot-strike pattern and alter the distribution of mechanical work at the knee and ankle joints when running at a fast speed in minimalist shoes compared with conventional running shoes. Crossover study. Research laboratory. Twenty-six trained runners (age = 30.0 ± 7.9 years [age range, 18-40 years], height = 1.79 ± 0.06 m, mass = 75.3 ± 8.2 kg, weekly training distance = 27 ± 15 km) who ran with a habitual rearfoot foot-strike pattern and had no experience running in minimalist shoes. Participants completed overground running trials at 18 km/h in minimalist and conventional shoes. Sagittal-plane kinematics and joint work at the knee and ankle joints were computed using 3-dimensional kinematic and ground reaction force data. Foot-strike pattern was classified as rearfoot, midfoot, or forefoot strike based on strike index and ankle angle at initial contact. We observed no difference in foot-strike classification between shoes (χ 2 1 = 2.29, P = .13). Ankle angle at initial contact was less (2.46° versus 7.43°; t 25 = 3.34, P = .003) and strike index was greater (35.97% versus 29.04%; t 25 = 2.38, P = .03) when running in minimalist shoes compared with conventional shoes. We observed greater negative (52.87 J versus 42.46 J; t 24 = 2.29, P = .03) and positive work (68.91 J versus 59.08 J; t 24 = 2.65, P = .01) at the ankle but less negative (59.01 J versus 67.02 J; t 24 = 2.25, P = .03) and positive work (40.37 J versus 47.09 J; t 24 = 2.11, P = .046) at the knee with minimalist shoes compared with conventional shoes. Running in minimalist shoes at a fast speed caused a redistribution of work from the knee to the ankle joint. This finding suggests that runners changing from conventional to minimalist shoes for short-distance races could be at an increased risk of ankle and calf injuries but a reduced risk of knee injuries.

Positive Selection Underlies Faster-Z Evolution of Gene Expression in Birds

PubMed Central

Dean, Rebecca; Harrison, Peter W.; Wright, Alison E.; Zimmer, Fabian; Mank, Judith E.

2015-01-01

The elevated rate of evolution for genes on sex chromosomes compared with autosomes (Fast-X or Fast-Z evolution) can result either from positive selection in the heterogametic sex or from nonadaptive consequences of reduced relative effective population size. Recent work in birds suggests that Fast-Z of coding sequence is primarily due to relaxed purifying selection resulting from reduced relative effective population size. However, gene sequence and gene expression are often subject to distinct evolutionary pressures; therefore, we tested for Fast-Z in gene expression using next-generation RNA-sequencing data from multiple avian species. Similar to studies of Fast-Z in coding sequence, we recover clear signatures of Fast-Z in gene expression; however, in contrast to coding sequence, our data indicate that Fast-Z in expression is due to positive selection acting primarily in females. In the soma, where gene expression is highly correlated between the sexes, we detected Fast-Z in both sexes, although at a higher rate in females, suggesting that many positively selected expression changes in females are also expressed in males. In the gonad, where intersexual correlations in expression are much lower, we detected Fast-Z for female gene expression, but crucially, not males. This suggests that a large amount of expression variation is sex-specific in its effects within the gonad. Taken together, our results indicate that Fast-Z evolution of gene expression is the product of positive selection acting on recessive beneficial alleles in the heterogametic sex. More broadly, our analysis suggests that the adaptive potential of Z chromosome gene expression may be much greater than that of gene sequence, results which have important implications for the role of sex chromosomes in speciation and sexual selection. PMID:26067773

Dual-comb spectroscopy of water vapor with a free-running semiconductor disk laser.

PubMed

Link, S M; Maas, D J H C; Waldburger, D; Keller, U

2017-06-16

Dual-comb spectroscopy offers the potential for high accuracy combined with fast data acquisition. Applications are often limited, however, by the complexity of optical comb systems. Here we present dual-comb spectroscopy of water vapor using a substantially simplified single-laser system. Very good spectroscopy measurements with fast sampling rates are achieved with a free-running dual-comb mode-locked semiconductor disk laser. The absolute stability of the optical comb modes is characterized both for free-running operation and with simple microwave stabilization. This approach drastically reduces the complexity for dual-comb spectroscopy. Band-gap engineering to tune the center wavelength from the ultraviolet to the mid-infrared could optimize frequency combs for specific gas targets, further enabling dual-comb spectroscopy for a wider range of industrial applications. Copyright © 2017, American Association for the Advancement of Science.

AlgoRun: a Docker-based packaging system for platform-agnostic implemented algorithms.

PubMed

Hosny, Abdelrahman; Vera-Licona, Paola; Laubenbacher, Reinhard; Favre, Thibauld

2016-08-01

There is a growing need in bioinformatics for easy-to-use software implementations of algorithms that are usable across platforms. At the same time, reproducibility of computational results is critical and often a challenge due to source code changes over time and dependencies. The approach introduced in this paper addresses both of these needs with AlgoRun, a dedicated packaging system for implemented algorithms, using Docker technology. Implemented algorithms, packaged with AlgoRun, can be executed through a user-friendly interface directly from a web browser or via a standardized RESTful web API to allow easy integration into more complex workflows. The packaged algorithm includes the entire software execution environment, thereby eliminating the common problem of software dependencies and the irreproducibility of computations over time. AlgoRun-packaged algorithms can be published on http://algorun.org, a centralized searchable directory to find existing AlgoRun-packaged algorithms. AlgoRun is available at http://algorun.org and the source code under GPL license is available at https://github.com/algorun laubenbacher@uchc.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Fast and Flexible Successive-Cancellation List Decoders for Polar Codes

NASA Astrophysics Data System (ADS)

Hashemi, Seyyed Ali; Condo, Carlo; Gross, Warren J.

2017-11-01

Polar codes have gained significant amount of attention during the past few years and have been selected as a coding scheme for the next generation of mobile broadband standard. Among decoding schemes, successive-cancellation list (SCL) decoding provides a reasonable trade-off between the error-correction performance and hardware implementation complexity when used to decode polar codes, at the cost of limited throughput. The simplified SCL (SSCL) and its extension SSCL-SPC increase the speed of decoding by removing redundant calculations when encountering particular information and frozen bit patterns (rate one and single parity check codes), while keeping the error-correction performance unaltered. In this paper, we improve SSCL and SSCL-SPC by proving that the list size imposes a specific number of bit estimations required to decode rate one and single parity check codes. Thus, the number of estimations can be limited while guaranteeing exactly the same error-correction performance as if all bits of the code were estimated. We call the new decoding algorithms Fast-SSCL and Fast-SSCL-SPC. Moreover, we show that the number of bit estimations in a practical application can be tuned to achieve desirable speed, while keeping the error-correction performance almost unchanged. Hardware architectures implementing both algorithms are then described and implemented: it is shown that our design can achieve 1.86 Gb/s throughput, higher than the best state-of-the-art decoders.

Antiplagiarism Software Takes on the Honor Code

ERIC Educational Resources Information Center

Wasley, Paula

2008-01-01

Among the 100-odd colleges with academic honor codes, plagiarism-detection services raise a knotty problem: Is software compatible with a system based on trust? The answer frequently devolves to the size and culture of the university. Colleges with traditional student-run honor codes tend to "forefront" trust, emphasizing it above all else. This…

Support for Debugging Automatically Parallelized Programs

NASA Technical Reports Server (NTRS)

Hood, Robert; Jost, Gabriele

2001-01-01

This viewgraph presentation provides information on support sources available for the automatic parallelization of computer program. CAPTools, a support tool developed at the University of Greenwich, transforms, with user guidance, existing sequential Fortran code into parallel message passing code. Comparison routines are then run for debugging purposes, in essence, ensuring that the code transformation was accurate.

Smoothed Particle Hydrodynamic Simulator

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

2016-10-05

This code is a highly modular framework for developing smoothed particle hydrodynamic (SPH) simulations running on parallel platforms. The compartmentalization of the code allows for rapid development of new SPH applications and modifications of existing algorithms. The compartmentalization also allows changes in one part of the code used by many applications to instantly be made available to all applications.

runDM: Running couplings of Dark Matter to the Standard Model

NASA Astrophysics Data System (ADS)

D'Eramo, Francesco; Kavanagh, Bradley J.; Panci, Paolo

2018-02-01

runDM calculates the running of the couplings of Dark Matter (DM) to the Standard Model (SM) in simplified models with vector mediators. By specifying the mass of the mediator and the couplings of the mediator to SM fields at high energy, the code can calculate the couplings at low energy, taking into account the mixing of all dimension-6 operators. runDM can also extract the operator coefficients relevant for direct detection, namely low energy couplings to up, down and strange quarks and to protons and neutrons.

Simutaneous Variational Retrievals of Temperature, Humidity, Surface and Cloud Properties from Satellite and Airborne Hyperspectral Infrared Sounder Data using the Havemann-Taylor Fast Radiative Transfer Code (HT-FRTC) as the Forward Model Operator

NASA Astrophysics Data System (ADS)

Havemann, S.; Thelen, J. C.; Harlow, R. C.

2016-12-01

Full scattering radiative transfer simulations for hyperspectral infrared and shortwave sounders are essential in order to be able to extract the maximal information content from these instruments for cloudy scenes and those with significant aerosol loading, but have been rarely done because of the high computational demands. The Havemann-Taylor Fast Radiative Transfer Code works in Principal Component space, reducing the computational demand by orders of magnitude thereby making fast simultaneous retrievals of vertical profiles of temperature and humidity, surface temperature and emissivity as well as cloud and aerosol properties feasible. Results of successful retrievals using IASI sounder data as well as data taken during flights of the Airborne Research Interferometer Evaluation System (ARIES) on board the FAAM Bae 146 aircraft will be presented. These will demonstrate that the use of all the instrument channels in PC space can provide valuable information both on temperature and humidity profiles relevant for NWP and on the cirrus cloud properties at the same time. There is very significant information on the humidity profile below semi-transparent cirrus to be gained from IR sounder data. The retrieved ice water content is in good agreement with airborne in-situ measurements during Lagrangian spiral descents. In addition to the full scattering calculations, the HT-FRTC has also been trained with a fast approximation to the scattering problem which reduces it to a clear-sky calculation but with a modified extinction (Chou scaling). Chou scaling is a reasonable approximation in the infrared but is very poor where the solar contribution becomes significant. The comparison of the retrieval performance with the full scattering solution and the Chou scaling solution in the forward model operator for infrared sounders shows that temperature and humidity profiles are only marginally degraded by the use of the Chou scaling approximation. Retrievals of the specific cloud parameters (ice water content, cirrus cloud thickness and cirrus cloud horizontal fraction) are however strongly negatively affected under the Chou scaling approximation. The aim is also to use HT-FRTC to run clear and cloudy simulations for the atmospheric state test set which has been prepared by the NASA/JPL/AIRS project.

Distributed Adaptive Binary Quantization for Fast Nearest Neighbor Search.

PubMed

Xianglong Liu; Zhujin Li; Cheng Deng; Dacheng Tao

2017-11-01

Hashing has been proved an attractive technique for fast nearest neighbor search over big data. Compared with the projection based hashing methods, prototype-based ones own stronger power to generate discriminative binary codes for the data with complex intrinsic structure. However, existing prototype-based methods, such as spherical hashing and K-means hashing, still suffer from the ineffective coding that utilizes the complete binary codes in a hypercube. To address this problem, we propose an adaptive binary quantization (ABQ) method that learns a discriminative hash function with prototypes associated with small unique binary codes. Our alternating optimization adaptively discovers the prototype set and the code set of a varying size in an efficient way, which together robustly approximate the data relations. Our method can be naturally generalized to the product space for long hash codes, and enjoys the fast training linear to the number of the training data. We further devise a distributed framework for the large-scale learning, which can significantly speed up the training of ABQ in the distributed environment that has been widely deployed in many areas nowadays. The extensive experiments on four large-scale (up to 80 million) data sets demonstrate that our method significantly outperforms state-of-the-art hashing methods, with up to 58.84% performance gains relatively.

High-Performance Computing and Visualization of Tsunamis and Wind-Driven Waves

NASA Astrophysics Data System (ADS)

Liu, Y. S.; Zhang, H.; Yuen, D. A.; Wang, M.

2005-12-01

The Sumatran earthquake and the tsunami waves produced have awakened great scientific interest in wave-propagation over undulated bottom topography and along complicated coastlines. The recent hurricane Katrina has also called our attention to shorter period waves near the coast. Analytical approximations are valid over long wavelengths in the far field. For near field regions with complex geography and other complications, such as islands and harbors, numerical simulations must be employed to obtain accurate predictions in time and space. Nowadays using 10**7 to 10**8 grid points become quite routine with massively parallel computers and large RAM and disk memories. Besides tsunamis, river discharges from upstream events and waves driven by hurricanes are also of societal relevance, especially in central China and now also in U.S.A. Using automatic grid generation methods, we have devised a finite-element based code, for the three stages which culminates with the use of the augmented Lagrangian method for the run-up process, as well as the Arbitrary Lagrange- Euler Configuration method to tackle the free surface problem near the seashore. This formulation allows for the wave surface to be self-consistently determined within a linearized framework and is computationally very fast. Our continuous efforts are focussed on seeking novel algorithms and state of art techniques, in order to unravel the mysteries associated with tsunami wave propagation and wind-driven waves in 3-D. We have cast the Navier-Stokes equations within the framework of a compressible model with an equation of state for sea-water. Our formulation allows the tracking and simulation of three stages , principally the formation, propagation and run-up stages of tsunami and waves coming ashore. The sequential version of this code can run on a workstation with 4 Gbyte memory less than 2 minutes per time step for one million grid points. This code has also been parallelized with MPI-2 and has good scaling properties, nearly linear speedup, which has been tested on a 32-node PC cluster. We have employed the actual ocean seafloor topographical data to construct oceanic volume and attempt to construct the coastline as realistic as possible, using 11 levels structure meshes in the radial direction of the earth. In order to understand the intricate dynamics of the wave interactions, we have implemented a visualization overlay based on Amira, a 3-D volume rendering visualization tools for massive data post-processing. The ability to visualize the large data sets remotely is an important objective we are aiming for, as international collaboration is one of the top aims of this research.

Reduction of PAPR in coded OFDM using fast Reed-Solomon codes over prime Galois fields

NASA Astrophysics Data System (ADS)

Motazedi, Mohammad Reza; Dianat, Reza

2017-02-01

In this work, two new techniques using Reed-Solomon (RS) codes over GF(257) and GF(65,537) are proposed for peak-to-average power ratio (PAPR) reduction in coded orthogonal frequency division multiplexing (OFDM) systems. The lengths of these codes are well-matched to the length of OFDM frames. Over these fields, the block lengths of codes are powers of two and we fully exploit the radix-2 fast Fourier transform algorithms. Multiplications and additions are simple modulus operations. These codes provide desirable randomness with a small perturbation in information symbols that is essential for generation of different statistically independent candidates. Our simulations show that the PAPR reduction ability of RS codes is the same as that of conventional selected mapping (SLM), but contrary to SLM, we can get error correction capability. Also for the second proposed technique, the transmission of side information is not needed. To the best of our knowledge, this is the first work using RS codes for PAPR reduction in single-input single-output systems.

Be Active Your Way: A Guide for Adults

MedlinePlus

... try): ❑ Aerobic dance ❑ Basketball ❑ Fast dancing ❑ Jumping rope ❑ Martial arts (such as karate) ❑ Race walking, jogging, or running ❑ ... Heavy gardening (digging,hoeing) • Hiking uphill • Jumping rope • Martial arts (such as karate) • Race walking,jogging,or running • ...

The Need for Vendor Source Code at NAS. Revised

NASA Technical Reports Server (NTRS)

Carter, Russell; Acheson, Steve; Blaylock, Bruce; Brock, David; Cardo, Nick; Ciotti, Bob; Poston, Alan; Wong, Parkson; Chancellor, Marisa K. (Technical Monitor)

1997-01-01

The Numerical Aerodynamic Simulation (NAS) Facility has a long standing practice of maintaining buildable source code for installed hardware. There are two reasons for this: NAS's designated pathfinding role, and the need to maintain a smoothly running operational capacity given the widely diversified nature of the vendor installations. NAS has a need to maintain support capabilities when vendors are not able; diagnose and remedy hardware or software problems where applicable; and to support ongoing system software development activities whether or not the relevant vendors feel support is justified. This note provides an informal history of these activities at NAS, and brings together the general principles that drive the requirement that systems integrated into the NAS environment run binaries built from source code, onsite.

Vectorization of a classical trajectory code on a floating point systems, Inc. Model 164 attached processor.

PubMed

Kraus, Wayne A; Wagner, Albert F

1986-04-01

A triatomic classical trajectory code has been modified by extensive vectorization of the algorithms to achieve much improved performance on an FPS 164 attached processor. Extensive timings on both the FPS 164 and a VAX 11/780 with floating point accelerator are presented as a function of the number of trajectories simultaneously run. The timing tests involve a potential energy surface of the LEPS variety and trajectories with 1000 time steps. The results indicate that vectorization results in timing improvements on both the VAX and the FPS. For larger numbers of trajectories run simultaneously, up to a factor of 25 improvement in speed occurs between VAX and FPS vectorized code. Copyright © 1986 John Wiley & Sons, Inc.

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.

Working research codes into fluid dynamics education: a science gateway approach

NASA Astrophysics Data System (ADS)

Mason, Lachlan; Hetherington, James; O'Reilly, Martin; Yong, May; Jersakova, Radka; Grieve, Stuart; Perez-Suarez, David; Klapaukh, Roman; Craster, Richard V.; Matar, Omar K.

2017-11-01

Research codes are effective for illustrating complex concepts in educational fluid dynamics courses, compared to textbook examples, an interactive three-dimensional visualisation can bring a problem to life! Various barriers, however, prevent the adoption of research codes in teaching: codes are typically created for highly-specific `once-off' calculations and, as such, have no user interface and a steep learning curve. Moreover, a code may require access to high-performance computing resources that are not readily available in the classroom. This project allows academics to rapidly work research codes into their teaching via a minimalist `science gateway' framework. The gateway is a simple, yet flexible, web interface allowing students to construct and run simulations, as well as view and share their output. Behind the scenes, the common operations of job configuration, submission, monitoring and post-processing are customisable at the level of shell scripting. In this talk, we demonstrate the creation of an example teaching gateway connected to the Code BLUE fluid dynamics software. Student simulations can be run via a third-party cloud computing provider or a local high-performance cluster. EPSRC, UK, MEMPHIS program Grant (EP/K003976/1), RAEng Research Chair (OKM).

Visual Computing Environment

NASA Technical Reports Server (NTRS)

Lawrence, Charles; Putt, Charles W.

1997-01-01

The Visual Computing Environment (VCE) is a NASA Lewis Research Center project to develop 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. The objectives of VCE are to (1) develop a visual computing environment for controlling the execution of individual simulation codes that are running in parallel and are distributed on heterogeneous host machines in a networked environment, (2) develop numerical coupling algorithms for interchanging boundary conditions between codes with arbitrary grid matching and different levels of dimensionality, (3) provide a graphical interface for simulation setup and control, and (4) provide tools for online visualization and plotting. VCE was designed to provide a distributed, object-oriented environment. Mechanisms are provided for creating and manipulating objects, such as grids, boundary conditions, and solution data. This environment includes parallel virtual machine (PVM) for distributed processing. Users can interactively select and couple any set of codes that have been modified to run in a parallel distributed fashion on a cluster of heterogeneous workstations. A scripting facility allows users to dictate the sequence of events that make up the particular simulation.

Endurance running ability at adolescence as a predictor of blood pressure levels and hypertension in men: a 25-year follow-up study.

PubMed

Mikkelsson, L; Kaprio, J; Kautiainen, H; Nupponen, H; Tikkanen, M J; Kujala, U M

2005-01-01

The aim was to study whether aerobic fitness measured by a maximal endurance running test at adolescence predicts prevalence of hypertension or blood pressure levels in adulthood. From the 413 (197 slow runners and 216 fast runners) participating in a 2000-meter running test at adolescence in 1976 and responding to a health and fitness questionnaire in 2001, 29 subjects (15 very slow runners and 14 very fast runners) participated in a clinical follow-up study in 2001. Compared to those who were fast runners in adolescence, those who were slow runners tended to have higher age-adjusted risk of hypertension at follow-up (OR 2.7, 95 % CI 0.9 to 7.5; p=0.07). The result persisted after further adjustment for body mass index at follow-up (OR 2.9, 95 % CI 1.0 to 8.3; p=0.05). Diastolic blood pressure was higher for very slow runners at adolescence compared to very fast runners, the age-adjusted mean diastolic blood pressure being 90 mm Hg (95 % CI 86 to 93) vs. 83 mm Hg (95 % CI 80 to 87), age-adjusted p=0.013. High endurance type fitness in adolescence predicts low risk of hypertension and low resting diastolic blood pressure levels in adult men.

Structure and software tools of AIDA.

PubMed

Duisterhout, J S; Franken, B; Witte, F

1987-01-01

AIDA consists of a set of software tools to allow for fast development and easy-to-maintain Medical Information Systems. AIDA supports all aspects of such a system both during development and operation. It contains tools to build and maintain forms for interactive data entry and on-line input validation, a database management system including a data dictionary and a set of run-time routines for database access, and routines for querying the database and output formatting. Unlike an application generator, the user of AIDA may select parts of the tools to fulfill his needs and program other subsystems not developed with AIDA. The AIDA software uses as host language the ANSI-standard programming language MUMPS, an interpreted language embedded in an integrated database and programming environment. This greatly facilitates the portability of AIDA applications. The database facilities supported by AIDA are based on a relational data model. This data model is built on top of the MUMPS database, the so-called global structure. This relational model overcomes the restrictions of the global structure regarding string length. The global structure is especially powerful for sorting purposes. Using MUMPS as a host language allows the user an easy interface between user-defined data validation checks or other user-defined code and the AIDA tools. AIDA has been designed primarily for prototyping and for the construction of Medical Information Systems in a research environment which requires a flexible approach. The prototyping facility of AIDA operates terminal independent and is even to a great extent multi-lingual. Most of these features are table-driven; this allows on-line changes in the use of terminal type and language, but also causes overhead. AIDA has a set of optimizing tools by which it is possible to build a faster, but (of course) less flexible code from these table definitions. By separating the AIDA software in a source and a run-time version, one is able to write implementation-specific code which can be selected and loaded by a special source loader, being part of the AIDA software. This feature is also accessible for maintaining software on different sites and on different installations.

Beyond filtered backprojection: A reconstruction software package for ion beam microtomography data

NASA Astrophysics Data System (ADS)

Habchi, C.; Gordillo, N.; Bourret, S.; Barberet, Ph.; Jovet, C.; Moretto, Ph.; Seznec, H.

2013-01-01

A new version of the TomoRebuild data reduction software package is presented, for the reconstruction of scanning transmission ion microscopy tomography (STIMT) and particle induced X-ray emission tomography (PIXET) images. First, we present a state of the art of the reconstruction codes available for ion beam microtomography. The algorithm proposed here brings several advantages. It is a portable, multi-platform code, designed in C++ with well-separated classes for easier use and evolution. Data reduction is separated in different steps and the intermediate results may be checked if necessary. Although no additional graphic library or numerical tool is required to run the program as a command line, a user friendly interface was designed in Java, as an ImageJ plugin. All experimental and reconstruction parameters may be entered either through this plugin or directly in text format files. A simple standard format is proposed for the input of experimental data. Optional graphic applications using the ROOT interface may be used separately to display and fit energy spectra. Regarding the reconstruction process, the filtered backprojection (FBP) algorithm, already present in the previous version of the code, was optimized so that it is about 10 times as fast. In addition, Maximum Likelihood Expectation Maximization (MLEM) and its accelerated version Ordered Subsets Expectation Maximization (OSEM) algorithms were implemented. A detailed user guide in English is available. A reconstruction example of experimental data from a biological sample is given. It shows the capability of the code to reduce noise in the sinograms and to deal with incomplete data, which puts a new perspective on tomography using low number of projections or limited angle.

Cost-Effective Sequencing of Full-Length cDNA Clones Powered by a De Novo-Reference Hybrid Assembly

PubMed Central

Sugano, Sumio; Morishita, Shinichi; Suzuki, Yutaka

2010-01-01

Background Sequencing full-length cDNA clones is important to determine gene structures including alternative splice forms, and provides valuable resources for experimental analyses to reveal the biological functions of coded proteins. However, previous approaches for sequencing cDNA clones were expensive or time-consuming, and therefore, a fast and efficient sequencing approach was demanded. Methodology We developed a program, MuSICA 2, that assembles millions of short (36-nucleotide) reads collected from a single flow cell lane of Illumina Genome Analyzer to shotgun-sequence ∼800 human full-length cDNA clones. MuSICA 2 performs a hybrid assembly in which an external de novo assembler is run first and the result is then improved by reference alignment of shotgun reads. We compared the MuSICA 2 assembly with 200 pooled full-length cDNA clones finished independently by the conventional primer-walking using Sanger sequencers. The exon-intron structure of the coding sequence was correct for more than 95% of the clones with coding sequence annotation when we excluded cDNA clones insufficiently represented in the shotgun library due to PCR failure (42 out of 200 clones excluded), and the nucleotide-level accuracy of coding sequences of those correct clones was over 99.99%. We also applied MuSICA 2 to full-length cDNA clones from Toxoplasma gondii, to confirm that its ability was competent even for non-human species. Conclusions The entire sequencing and shotgun assembly takes less than 1 week and the consumables cost only ∼US$3 per clone, demonstrating a significant advantage over previous approaches. PMID:20479877

Qualification of Simulation Software for Safety Assessment of Sodium Cooled Fast Reactors. Requirements and Recommendations

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

Brown, Nicholas R.; Pointer, William David; Sieger, Matt

2016-04-01

The goal of this review is to enable application of codes or software packages for safety assessment of advanced sodium-cooled fast reactor (SFR) designs. To address near-term programmatic needs, the authors have focused on two objectives. First, the authors have focused on identification of requirements for software QA that must be satisfied to enable the application of software to future safety analyses. Second, the authors have collected best practices applied by other code development teams to minimize cost and time of initial code qualification activities and to recommend a path to the stated goal.

Variable disparity-motion estimation based fast three-view video coding

NASA Astrophysics Data System (ADS)

Bae, Kyung-Hoon; Kim, Seung-Cheol; Hwang, Yong Seok; Kim, Eun-Soo

2009-02-01

In this paper, variable disparity-motion estimation (VDME) based 3-view video coding is proposed. In the encoding, key-frame coding (KFC) based motion estimation and variable disparity estimation (VDE) for effectively fast three-view video encoding are processed. These proposed algorithms enhance the performance of 3-D video encoding/decoding system in terms of accuracy of disparity estimation and computational overhead. From some experiments, stereo sequences of 'Pot Plant' and 'IVO', it is shown that the proposed algorithm's PSNRs is 37.66 and 40.55 dB, and the processing time is 0.139 and 0.124 sec/frame, respectively.

FRUIT: An operational tool for multisphere neutron spectrometry in workplaces

NASA Astrophysics Data System (ADS)

Bedogni, Roberto; Domingo, Carles; Esposito, Adolfo; Fernández, Francisco

2007-10-01

FRUIT (Frascati Unfolding Interactive Tool) is an unfolding code for Bonner sphere spectrometers (BSS) developed, under the Labview environment, at the INFN-Frascati National Laboratory. It models a generic neutron spectrum as the superposition of up to four components (thermal, epithermal, fast and high energy), fully defined by up to seven positive parameters. Different physical models are available to unfold the sphere counts, covering the majority of the neutron spectra encountered in workplaces. The iterative algorithm uses Monte Carlo methods to vary the parameters and derive the final spectrum as limit of a succession of spectra fulfilling the established convergence criteria. Uncertainties on the final results are evaluated taking into consideration the different sources of uncertainty affecting the input data. Relevant features of FRUIT are (1) a high level of interactivity, allowing the user to follow the convergence process, (2) the possibility to modify the convergence tolerances during the run, allowing a rapid achievement of meaningful solutions and (3) the reduced dependence of the results from the initial hypothesis. This provides a useful instrument for spectrometric measurements in workplaces, where detailed a priori information is usually unavailable. This paper describes the characteristics of the code and presents the results of performance tests over a significant variety of reference and workplace neutron spectra ranging from thermal up to hundreds MeV neutrons.

Volumetric Real-Time Imaging Using a CMUT Ring Array

PubMed Central

Choe, Jung Woo; Oralkan, Ömer; Nikoozadeh, Amin; Gencel, Mustafa; Stephens, Douglas N.; O’Donnell, Matthew; Sahn, David J.; Khuri-Yakub, Butrus T.

2012-01-01

A ring array provides a very suitable geometry for forward-looking volumetric intracardiac and intravascular ultrasound imaging. We fabricated an annular 64-element capacitive micromachined ultrasonic transducer (CMUT) array featuring a 10-MHz operating frequency and a 1.27-mm outer radius. A custom software suite was developed to run on a PC-based imaging system for real-time imaging using this device. This paper presents simulated and experimental imaging results for the described CMUT ring array. Three different imaging methods—flash, classic phased array (CPA), and synthetic phased array (SPA)—were used in the study. For SPA imaging, two techniques to improve the image quality—Hadamard coding and aperture weighting—were also applied. The results show that SPA with Hadamard coding and aperture weighting is a good option for ring-array imaging. Compared with CPA, it achieves better image resolution and comparable signal-to-noise ratio at a much faster image acquisition rate. Using this method, a fast frame rate of up to 463 volumes per second is achievable if limited only by the ultrasound time of flight; with the described system we reconstructed three cross-sectional images in real-time at 10 frames per second, which was limited by the computation time in synthetic beamforming. PMID:22718870

Geant4 Computing Performance Benchmarking and Monitoring

DOE PAGES

Dotti, Andrea; Elvira, V. Daniel; Folger, Gunter; ...

2015-12-23

Performance evaluation and analysis of large scale computing applications is essential for optimal use of resources. As detector simulation is one of the most compute intensive tasks and Geant4 is the simulation toolkit most widely used in contemporary high energy physics (HEP) experiments, it is important to monitor Geant4 through its development cycle for changes in computing performance and to identify problems and opportunities for code improvements. All Geant4 development and public releases are being profiled with a set of applications that utilize different input event samples, physics parameters, and detector configurations. Results from multiple benchmarking runs are compared tomore » previous public and development reference releases to monitor CPU and memory usage. Observed changes are evaluated and correlated with code modifications. Besides the full summary of call stack and memory footprint, a detailed call graph analysis is available to Geant4 developers for further analysis. The set of software tools used in the performance evaluation procedure, both in sequential and multi-threaded modes, include FAST, IgProf and Open|Speedshop. In conclusion, the scalability of the CPU time and memory performance in multi-threaded application is evaluated by measuring event throughput and memory gain as a function of the number of threads for selected event samples.« less

GPU.proton.DOCK: Genuine Protein Ultrafast proton equilibria consistent DOCKing.

PubMed

Kantardjiev, Alexander A

2011-07-01

GPU.proton.DOCK (Genuine Protein Ultrafast proton equilibria consistent DOCKing) is a state of the art service for in silico prediction of protein-protein interactions via rigorous and ultrafast docking code. It is unique in providing stringent account of electrostatic interactions self-consistency and proton equilibria mutual effects of docking partners. GPU.proton.DOCK is the first server offering such a crucial supplement to protein docking algorithms--a step toward more reliable and high accuracy docking results. The code (especially the Fast Fourier Transform bottleneck and electrostatic fields computation) is parallelized to run on a GPU supercomputer. The high performance will be of use for large-scale structural bioinformatics and systems biology projects, thus bridging physics of the interactions with analysis of molecular networks. We propose workflows for exploring in silico charge mutagenesis effects. Special emphasis is given to the interface-intuitive and user-friendly. The input is comprised of the atomic coordinate files in PDB format. The advanced user is provided with a special input section for addition of non-polypeptide charges, extra ionogenic groups with intrinsic pK(a) values or fixed ions. The output is comprised of docked complexes in PDB format as well as interactive visualization in a molecular viewer. GPU.proton.DOCK server can be accessed at http://gpudock.orgchm.bas.bg/.

Volumetric real-time imaging using a CMUT ring array.

PubMed

Choe, Jung Woo; Oralkan, Ömer; Nikoozadeh, Amin; Gencel, Mustafa; Stephens, Douglas N; O'Donnell, Matthew; Sahn, David J; Khuri-Yakub, Butrus T

2012-06-01

A ring array provides a very suitable geometry for forward-looking volumetric intracardiac and intravascular ultrasound imaging. We fabricated an annular 64-element capacitive micromachined ultrasonic transducer (CMUT) array featuring a 10-MHz operating frequency and a 1.27-mm outer radius. A custom software suite was developed to run on a PC-based imaging system for real-time imaging using this device. This paper presents simulated and experimental imaging results for the described CMUT ring array. Three different imaging methods--flash, classic phased array (CPA), and synthetic phased array (SPA)--were used in the study. For SPA imaging, two techniques to improve the image quality--Hadamard coding and aperture weighting--were also applied. The results show that SPA with Hadamard coding and aperture weighting is a good option for ring-array imaging. Compared with CPA, it achieves better image resolution and comparable signal-to-noise ratio at a much faster image acquisition rate. Using this method, a fast frame rate of up to 463 volumes per second is achievable if limited only by the ultrasound time of flight; with the described system we reconstructed three cross-sectional images in real-time at 10 frames per second, which was limited by the computation time in synthetic beamforming.

A comparison of five benchmarks

NASA Technical Reports Server (NTRS)

Huss, Janice E.; Pennline, James A.

1987-01-01

Five benchmark programs were obtained and run on the NASA Lewis CRAY X-MP/24. A comparison was made between the programs codes and between the methods for calculating performance figures. Several multitasking jobs were run to gain experience in how parallel performance is measured.

Simulation with EGS4 code of external beam of radiotherapy apparatus with workstation and PC gives similar results?

PubMed

Malataras, G; Kappas, C; Lovelock, D M; Mohan, R

1997-01-01

This article presents a comparison between two implementations of an EGS4 Monte Carlo simulation of a radiation therapy machine. The first implementation was run on a high performance RISC workstation, and the second was run on an inexpensive PC. The simulation was performed using the MCRAD user code. The photon energy spectra, as measured at a plane transverse to the beam direction and containing the isocenter, were compared. The photons were also binned radially in order to compare the variation of the spectra with radius. With 500,000 photons recorded in each of the two simulations, the running times were 48 h and 116 h for the workstation and the PC, respectively. No significant statistical differences between the two implementations were found.

Secure web-based invocation of large-scale plasma simulation codes

NASA Astrophysics Data System (ADS)

Dimitrov, D. A.; Busby, R.; Exby, J.; Bruhwiler, D. L.; Cary, J. R.

2004-12-01

We present our design and initial implementation of a web-based system for running, both in parallel and serial, Particle-In-Cell (PIC) codes for plasma simulations with automatic post processing and generation of visual diagnostics.

Scalable Technology for a New Generation of Collaborative Applications

DTIC Science & Technology

2007-04-01

of the International Symposium on Distributed Computing (DISC), Cracow, Poland, September 2005. Classic Paxos vs. Fast Paxos: Caveat Emptor, Flavio...grou or able and fast multicast primitive to layer under high-level latency across dimensions as varied as group size [10, 17],abstractions such as...servers, networked via fast , dedicated interconnects. The system to subscribe to a fraction of the equities on the software stack running on a single

Dynamic multistation photometer

DOEpatents

Bauer, Martin L.; Johnson, Wayne F.; Lakomy, Dale G.

1977-01-01

A portable fast analyzer is provided that uses a magnetic clutch/brake to rapidly accelerate the analyzer rotor, and employs a microprocessor for automatic analyzer operation. The rotor is held stationary while the drive motor is run up to speed. When it is desired to mix the sample(s) and reagent(s), the brake is deenergized and the clutch is energized wherein the rotor is very rapidly accelerated to the running speed. The parallel path rotor that is used allows the samples and reagents to be mixed the moment they are spun out into the rotor cuvetes and data acquisition begins immediately. The analyzer will thus have special utility for fast reactions.

Fast running restricts evolutionary change of the vertebral column in mammals.

PubMed

Galis, Frietson; Carrier, David R; van Alphen, Joris; van der Mije, Steven D; Van Dooren, Tom J M; Metz, Johan A J; ten Broek, Clara M A

2014-08-05

The mammalian vertebral column is highly variable, reflecting adaptations to a wide range of lifestyles, from burrowing in moles to flying in bats. However, in many taxa, the number of trunk vertebrae is surprisingly constant. We argue that this constancy results from strong selection against initial changes of these numbers in fast running and agile mammals, whereas such selection is weak in slower-running, sturdier mammals. The rationale is that changes of the number of trunk vertebrae require homeotic transformations from trunk into sacral vertebrae, or vice versa, and mutations toward such transformations generally produce transitional lumbosacral vertebrae that are incompletely fused to the sacrum. We hypothesize that such incomplete homeotic transformations impair flexibility of the lumbosacral joint and thereby threaten survival in species that depend on axial mobility for speed and agility. Such transformations will only marginally affect performance in slow, sturdy species, so that sufficient individuals with transitional vertebrae survive to allow eventual evolutionary changes of trunk vertebral numbers. We present data on fast and slow carnivores and artiodactyls and on slow afrotherians and monotremes that strongly support this hypothesis. The conclusion is that the selective constraints on the count of trunk vertebrae stem from a combination of developmental and biomechanical constraints.

HT-FRTC: a fast radiative transfer code using kernel regression

NASA Astrophysics Data System (ADS)

Thelen, Jean-Claude; Havemann, Stephan; Lewis, Warren

2016-09-01

The HT-FRTC is a principal component based fast radiative transfer code that can be used across the electromagnetic spectrum from the microwave through to the ultraviolet to calculate transmittance, radiance and flux spectra. The principal components cover the spectrum at a very high spectral resolution, which allows very fast line-by-line, hyperspectral and broadband simulations for satellite-based, airborne and ground-based sensors. The principal components are derived during a code training phase from line-by-line simulations for a diverse set of atmosphere and surface conditions. The derived principal components are sensor independent, i.e. no extra training is required to include additional sensors. During the training phase we also derive the predictors which are required by the fast radiative transfer code to determine the principal component scores from the monochromatic radiances (or fluxes, transmittances). These predictors are calculated for each training profile at a small number of frequencies, which are selected by a k-means cluster algorithm during the training phase. Until recently the predictors were calculated using a linear regression. However, during a recent rewrite of the code the linear regression was replaced by a Gaussian Process (GP) regression which resulted in a significant increase in accuracy when compared to the linear regression. The HT-FRTC has been trained with a large variety of gases, surface properties and scatterers. Rayleigh scattering as well as scattering by frozen/liquid clouds, hydrometeors and aerosols have all been included. The scattering phase function can be fully accounted for by an integrated line-by-line version of the Edwards-Slingo spherical harmonics radiation code or approximately by a modification to the extinction (Chou scaling).

Voluntary resistance running with short distance enhances spatial memory related to hippocampal BDNF signaling.

PubMed

Lee, Min Chul; Okamoto, Masahiro; Liu, Yu Fan; Inoue, Koshiro; Matsui, Takashi; Nogami, Haruo; Soya, Hideaki

2012-10-15

Although voluntary running has beneficial effects on hippocampal cognitive functions if done abundantly, it is still uncertain whether resistance running would be the same. For this purpose, voluntary resistance wheel running (RWR) with a load is a suitable model, since it allows increased work levels and resultant muscular adaptation in fast-twitch muscle. Here, we examined whether RWR would have potential effects on hippocampal cognitive functions with enhanced hippocampal brain-derived neurotrophic factor (BDNF), as does wheel running without a load (WR). Ten-week-old male Wistar rats were assigned randomly to sedentary (Sed), WR, and RWR (to a maximum load of 30% of body weight) groups for 4 wk. We found that in RWR, work levels increased with load, but running distance decreased by about half, which elicited muscular adaptation for fast-twitch plantaris muscle without causing any negative stress effects. Both RWR and WR led to improved spatial learning and memory as well as gene expressions of hippocampal BDNF signaling-related molecules. RWR increased hippocampal BDNF, tyrosine-related kinase B (TrkB), and cAMP response element-binding (CREB) protein levels, whereas WR increased only BDNF. With both exercise groups, there were correlations between spatial memory and BDNF protein (r = 0.41), p-CREB protein (r = 0.44), and work levels (r = 0.77). These results suggest that RWR plays a beneficial role in hippocampus-related cognitive functions associated with hippocampal BDNF signaling, even with short distances, and that work levels rather than running distance are more determinant of exercise-induced beneficial effects in wheel running with and without a load.

Fast Faraday cup for fast ion beam TOF measurements in deuterium filled plasma focus device and correlation with Lee model

NASA Astrophysics Data System (ADS)

Damideh, Vahid; Ali, Jalil; Saw, Sor Heoh; Rawat, Rajdeep Singh; Lee, Paul; Chaudhary, Kashif Tufail; Rizvi, Zuhaib Haider; Dabagh, Shadab; Ismail, Fairuz Diyana; Sing, Lee

2017-06-01

In this work, the design and construction of a 50 Ω fast Faraday cup and its results in correlation with the Lee Model Code for fast ion beam and ion time of flight measurements for a Deuterium filled plasma focus device are presented. Fast ion beam properties such as ion flux, fluence, speed, and energy at 2-8 Torr Deuterium are studied. The minimum 34 ns full width at half maximum ion signal at 12 kV, 3 Torr Deuterium in INTI PF was captured by a Faraday cup. The maximum ion energy of 67 ± 5 keV at 4 Torr Deuterium was detected by the Faraday cup. Ion time of flight measurements by the Faraday cup show consistent correlation with Lee Code results for Deuterium especially at near to optimum pressures.

A Loader for Executing Multi-Binary Applications on the Thinking Machines CM-5: It's Not Just for SPMD Anymore

NASA Technical Reports Server (NTRS)

Becker, Jeffrey C.

1995-01-01

The Thinking Machines CM-5 platform was designed to run single program, multiple data (SPMD) applications, i.e., to run a single binary across all nodes of a partition, with each node possibly operating on different data. Certain classes of applications, such as multi-disciplinary computational fluid dynamics codes, are facilitated by the ability to have subsets of the partition nodes running different binaries. In order to extend the CM-5 system software to permit such applications, a multi-program loader was developed. This system is based on the dld loader which was originally developed for workstations. This paper provides a high level description of dld, and describes how it was ported to the CM-5 to provide support for multi-binary applications. Finally, it elaborates how the loader has been used to implement the CM-5 version of MPIRUN, a portable facility for running multi-disciplinary/multi-zonal MPI (Message-Passing Interface Standard) codes.

A Concept for Run-Time Support of the Chapel Language

NASA Technical Reports Server (NTRS)

James, Mark

2006-01-01

A document presents a concept for run-time implementation of other concepts embodied in the Chapel programming language. (Now undergoing development, Chapel is intended to become a standard language for parallel computing that would surpass older such languages in both computational performance in the efficiency with which pre-existing code can be reused and new code written.) The aforementioned other concepts are those of distributions, domains, allocations, and access, as defined in a separate document called "A Semantic Framework for Domains and Distributions in Chapel" and linked to a language specification defined in another separate document called "Chapel Specification 0.3." The concept presented in the instant report is recognition that a data domain that was invented for Chapel offers a novel approach to distributing and processing data in a massively parallel environment. The concept is offered as a starting point for development of working descriptions of functions and data structures that would be necessary to implement interfaces to a compiler for transforming the aforementioned other concepts from their representations in Chapel source code to their run-time implementations.

Application of Fast Multipole Methods to the NASA Fast Scattering Code

NASA Technical Reports Server (NTRS)

Dunn, Mark H.; Tinetti, Ana F.

2008-01-01

The NASA Fast Scattering Code (FSC) is a versatile noise prediction program designed to conduct aeroacoustic noise reduction studies. The equivalent source method is used to solve an exterior Helmholtz boundary value problem with an impedance type boundary condition. The solution process in FSC v2.0 requires direct manipulation of a large, dense system of linear equations, limiting the applicability of the code to small scales and/or moderate excitation frequencies. Recent advances in the use of Fast Multipole Methods (FMM) for solving scattering problems, coupled with sparse linear algebra techniques, suggest that a substantial reduction in computer resource utilization over conventional solution approaches can be obtained. Implementation of the single level FMM (SLFMM) and a variant of the Conjugate Gradient Method (CGM) into the FSC is discussed in this paper. The culmination of this effort, FSC v3.0, was used to generate solutions for three configurations of interest. Benchmarking against previously obtained simulations indicate that a twenty-fold reduction in computational memory and up to a four-fold reduction in computer time have been achieved on a single processor.

The EUCLID/V1 Integrated Code for Safety Assessment of Liquid Metal Cooled Fast Reactors. Part 1: Basic Models

NASA Astrophysics Data System (ADS)

Mosunova, N. A.

2018-05-01

The article describes the basic models included in the EUCLID/V1 integrated code intended for safety analysis of liquid metal (sodium, lead, and lead-bismuth) cooled fast reactors using fuel rods with a gas gap and pellet dioxide, mixed oxide or nitride uranium-plutonium fuel under normal operation, under anticipated operational occurrences and accident conditions by carrying out interconnected thermal-hydraulic, neutronics, and thermal-mechanical calculations. Information about the Russian and foreign analogs of the EUCLID/V1 integrated code is given. Modeled objects, equation systems in differential form solved in each module of the EUCLID/V1 integrated code (the thermal-hydraulic, neutronics, fuel rod analysis module, and the burnup and decay heat calculation modules), the main calculated quantities, and also the limitations on application of the code are presented. The article also gives data on the scope of functions performed by the integrated code's thermal-hydraulic module, using which it is possible to describe both one- and twophase processes occurring in the coolant. It is shown that, owing to the availability of the fuel rod analysis module in the integrated code, it becomes possible to estimate the performance of fuel rods in different regimes of the reactor operation. It is also shown that the models implemented in the code for calculating neutron-physical processes make it possible to take into account the neutron field distribution over the fuel assembly cross section as well as other features important for the safety assessment of fast reactors.

Linearized Aeroelastic Solver Applied to the Flutter Prediction of Real Configurations

NASA Technical Reports Server (NTRS)

Reddy, Tondapu S.; Bakhle, Milind A.

2004-01-01

A fast-running unsteady aerodynamics code, LINFLUX, was previously developed for predicting turbomachinery flutter. This linearized code, based on a frequency domain method, models the effects of steady blade loading through a nonlinear steady flow field. The LINFLUX code, which is 6 to 7 times faster than the corresponding nonlinear time domain code, is suitable for use in the initial design phase. Earlier, this code was verified through application to a research fan, and it was shown that the predictions of work per cycle and flutter compared well with those from a nonlinear time-marching aeroelastic code, TURBO-AE. Now, the LINFLUX code has been applied to real configurations: fans developed under the Energy Efficient Engine (E-cubed) Program and the Quiet Aircraft Technology (QAT) project. The LINFLUX code starts with a steady nonlinear aerodynamic flow field and solves the unsteady linearized Euler equations to calculate the unsteady aerodynamic forces on the turbomachinery blades. First, a steady aerodynamic solution is computed for given operating conditions using the nonlinear unsteady aerodynamic code TURBO-AE. A blade vibration analysis is done to determine the frequencies and mode shapes of the vibrating blades, and an interface code is used to convert the steady aerodynamic solution to a form required by LINFLUX. A preprocessor is used to interpolate the mode shapes from the structural dynamics mesh onto the computational fluid dynamics mesh. Then, LINFLUX is used to calculate the unsteady aerodynamic pressure distribution for a given vibration mode, frequency, and interblade phase angle. Finally, a post-processor uses the unsteady pressures to calculate the generalized aerodynamic forces, eigenvalues, an esponse amplitudes. The eigenvalues determine the flutter frequency and damping. Results of flutter calculations from the LINFLUX code are presented for (1) the E-cubed fan developed under the E-cubed program and (2) the Quiet High Speed Fan (QHSF) developed under the Quiet Aircraft Technology project. The results are compared with those obtained from the TURBO-AE code. A graph of the work done per vibration cycle for the first vibration mode of the E-cubed fan is shown. It can be seen that the LINFLUX results show a very good comparison with TURBO-AE results over the entire range of interblade phase angle. The work done per vibration cycle for the first vibration mode of the QHSF fan is shown. Once again, the LINFLUX results compare very well with the results from the TURBOAE code.

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.

Fast Scattering Code (FSC) User's Manual: Version 2

NASA Technical Reports Server (NTRS)

Tinetti, Ana F.; Dun, M. H.; Pope, D. Stuart

2006-01-01

The Fast Scattering Code (version 2.0) is a computer program for predicting the three-dimensional scattered acoustic field produced by the interaction of known, time-harmonic, incident sound with aerostructures in the presence of potential background flow. The FSC has been developed for use as an aeroacoustic analysis tool for assessing global effects on noise radiation and scattering caused by changes in configuration (geometry, component placement) and operating conditions (background flow, excitation frequency).

Competitive code-based fast palmprint identification using a set of cover trees

NASA Astrophysics Data System (ADS)

Yue, Feng; Zuo, Wangmeng; Zhang, David; Wang, Kuanquan

2009-06-01

A palmprint identification system recognizes a query palmprint image by searching for its nearest neighbor from among all the templates in a database. When applied on a large-scale identification system, it is often necessary to speed up the nearest-neighbor searching process. We use competitive code, which has very fast feature extraction and matching speed, for palmprint identification. To speed up the identification process, we extend the cover tree method and propose to use a set of cover trees to facilitate the fast and accurate nearest-neighbor searching. We can use the cover tree method because, as we show, the angular distance used in competitive code can be decomposed into a set of metrics. Using the Hong Kong PolyU palmprint database (version 2) and a large-scale palmprint database, our experimental results show that the proposed method searches for nearest neighbors faster than brute force searching.

FAST: Fitting and Assessment of Synthetic Templates

NASA Astrophysics Data System (ADS)

Kriek, Mariska; van Dokkum, Pieter G.; Labbé, Ivo; Franx, Marijn; Illingworth, Garth D.; Marchesini, Danilo; Quadri, Ryan F.; Aird, James; Coil, Alison L.; Georgakakis, Antonis

2018-03-01

FAST (Fitting and Assessment of Synthetic Templates) fits stellar population synthesis templates to broadband photometry and/or spectra. FAST is compatible with the photometric redshift code EAzY (ascl:1010.052) when fitting broadband photometry; it uses the photometric redshifts derived by EAzY, and the input files (for examply, photometric catalog and master filter file) are the same. FAST fits spectra in combination with broadband photometric data points or simultaneously fits two components, allowing for an AGN contribution in addition to the host galaxy light. Depending on the input parameters, FAST outputs the best-fit redshift, age, dust content, star formation timescale, metallicity, stellar mass, star formation rate (SFR), and their confidence intervals. Though some of FAST's functions overlap with those of HYPERZ (ascl:1108.010), it differs by fitting fluxes instead of magnitudes, allows the user to completely define the grid of input stellar population parameters and easily input photometric redshifts and their confidence intervals, and calculates calibrated confidence intervals for all parameters. Note that FAST is not a photometric redshift code, though it can be used as one.

Coding the presence of visual objects in a recurrent neural network of visual cortex.

PubMed

Zwickel, Timm; Wachtler, Thomas; Eckhorn, Reinhard

2007-01-01

Before we can recognize a visual object, our visual system has to segregate it from its background. This requires a fast mechanism for establishing the presence and location of objects independently of their identity. Recently, border-ownership neurons were recorded in monkey visual cortex which might be involved in this task [Zhou, H., Friedmann, H., von der Heydt, R., 2000. Coding of border ownership in monkey visual cortex. J. Neurosci. 20 (17), 6594-6611]. In order to explain the basic mechanisms required for fast coding of object presence, we have developed a neural network model of visual cortex consisting of three stages. Feed-forward and lateral connections support coding of Gestalt properties, including similarity, good continuation, and convexity. Neurons of the highest area respond to the presence of an object and encode its position, invariant of its form. Feedback connections to the lowest area facilitate orientation detectors activated by contours belonging to potential objects, and thus generate the experimentally observed border-ownership property. This feedback control acts fast and significantly improves the figure-ground segregation required for the consecutive task of object recognition.

The Derivation of the Gradient of the Acoustic Pressure on a Moving Surface for Application to the Fast Scattering Code (FSC)

NASA Technical Reports Server (NTRS)

Farassat, F.; Brentner, Kenneth S.

2005-01-01

In this paper we develop an analytic expression for calculation of the the acoustic pressure from a rotating blade on a moving surface for application to the Fast Scattering Code (FSC). The analytic result is intended to be used in the helicopter noise prediction code PSU-WOPWOP. One of the goals of the derivation is obtaining a result that will not use any more information than are needed for the prediction of the thickness and loading noise. The result derived here achieves this goal and its incorporation in PSU-WOPWOP is straight forward and attainable.

Multitasking kernel for the C and Fortran programming languages

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

Brooks, E.D. III

1984-09-01

A multitasking kernel for the C and Fortran programming languages which runs on the Unix operating system is presented. The kernel provides a multitasking environment which serves two purposes. The first is to provide an efficient portable environment for the coding, debugging and execution of production multiprocessor programs. The second is to provide a means of evaluating the performance of a multitasking program on model multiprocessors. The performance evaluation features require no changes in the source code of the application and are implemented as a set of compile and run time options in the kernel.

Program MAMO: Models for avian management optimization-user guide

USGS Publications Warehouse

Guillaumet, Alban; Paxton, Eben H.

2017-01-01

The following chapters describe the structure and code of MAMO, and walk the reader through running the different components of the program with sample data. This manual should be used alongside a computer running R, so that the reader can copy and paste code into R, observe the output, and follow along interactively. Taken together, chapters 2–4 will allow the user to replicate a simulation study investigating the consequences of climate change and two potential management actions on the population dynamics of a vulnerable and iconic Hawaiian forest bird, the ‘I‘iwi (Drepanis coccinea; hereafter IIWI).

Open-Source Python Tools for Deploying Interactive GIS Dashboards for a Billion Datapoints on a Laptop

NASA Astrophysics Data System (ADS)

Steinberg, P. D.; Bednar, J. A.; Rudiger, P.; Stevens, J. L. R.; Ball, C. E.; Christensen, S. D.; Pothina, D.

2017-12-01

The rich variety of software libraries available in the Python scientific ecosystem provides a flexible and powerful alternative to traditional integrated GIS (geographic information system) programs. Each such library focuses on doing a certain set of general-purpose tasks well, and Python makes it relatively simple to glue the libraries together to solve a wide range of complex, open-ended problems in Earth science. However, choosing an appropriate set of libraries can be challenging, and it is difficult to predict how much "glue code" will be needed for any particular combination of libraries and tasks. Here we present a set of libraries that have been designed to work well together to build interactive analyses and visualizations of large geographic datasets, in standard web browsers. The resulting workflows run on ordinary laptops even for billions of data points, and easily scale up to larger compute clusters when available. The declarative top-level interface used in these libraries means that even complex, fully interactive applications can be built and deployed as web services using only a few dozen lines of code, making it simple to create and share custom interactive applications even for datasets too large for most traditional GIS systems. The libraries we will cover include GeoViews (HoloViews extended for geographic applications) for declaring visualizable/plottable objects, Bokeh for building visual web applications from GeoViews objects, Datashader for rendering arbitrarily large datasets faithfully as fixed-size images, Param for specifying user-modifiable parameters that model your domain, Xarray for computing with n-dimensional array data, Dask for flexibly dispatching computational tasks across processors, and Numba for compiling array-based Python code down to fast machine code. We will show how to use the resulting workflow with static datasets and with simulators such as GSSHA or AdH, allowing you to deploy flexible, high-performance web-based dashboards for your GIS data or simulations without needing major investments in code development or maintenance.

Japan’s Nuclear Future: Policy Debate, Prospects, and U.S. Interests

DTIC Science & Technology

2008-05-09

raised in particular over the construction of an industrial- scale reprocessing facility in Japan,. Additionally, fast breeder reactors also produce more...Nuclear Fuel Cycle Engineering Laboratories. 10 A fast breeder reactor is a fast neutron reactor that produces more plutonium than it consumes, which can...Japan Nuclear Fuel Limited (JNFL) has built and is currently running active testing on a large - scale commercial reprocessing plant at Rokkasho-mura

RAY-RAMSES: a code for ray tracing on the fly in N-body simulations

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

Barreira, Alexandre; Llinares, Claudio; Bose, Sownak

2016-05-01

We present a ray tracing code to compute integrated cosmological observables on the fly in AMR N-body simulations. Unlike conventional ray tracing techniques, our code takes full advantage of the time and spatial resolution attained by the N-body simulation by computing the integrals along the line of sight on a cell-by-cell basis through the AMR simulation grid. Moroever, since it runs on the fly in the N-body run, our code can produce maps of the desired observables without storing large (or any) amounts of data for post-processing. We implemented our routines in the RAMSES N-body code and tested the implementationmore » using an example of weak lensing simulation. We analyse basic statistics of lensing convergence maps and find good agreement with semi-analytical methods. The ray tracing methodology presented here can be used in several cosmological analysis such as Sunyaev-Zel'dovich and integrated Sachs-Wolfe effect studies as well as modified gravity. Our code can also be used in cross-checks of the more conventional methods, which can be important in tests of theory systematics in preparation for upcoming large scale structure surveys.« less

Fast Flows in the Magnetotail and Energetic Particle Transport: Multiscale Coupling in the Magnetosphere

NASA Astrophysics Data System (ADS)

Lin, Y.; Wang, X.; Fok, M. C. H.; Buzulukova, N.; Perez, J. D.; Chen, L. J.

2017-12-01

The interaction between the Earth's inner and outer magnetospheric regions associated with the tail fast flows is calculated by coupling the Auburn 3-D global hybrid simulation code (ANGIE3D) to the Comprehensive Inner Magnetosphere/Ionosphere (CIMI) model. The global hybrid code solves fully kinetic equations governing the ions and a fluid model for electrons in the self-consistent electromagnetic field of the dayside and night side outer magnetosphere. In the integrated computation model, the hybrid simulation provides the CIMI model with field data in the CIMI 3-D domain and particle data at its boundary, and the transport in the inner magnetosphere is calculated by the CIMI model. By joining the two existing codes, effects of the solar wind on particle transport through the outer magnetosphere into the inner magnetosphere are investigated. Our simulation shows that fast flows and flux ropes are localized transients in the magnetotail plasma sheet and their overall structures have a dawn-dusk asymmetry. Strong perpendicular ion heating is found at the fast flow braking, which affects the earthward transport of entropy-depleted bubbles. We report on the impacts from the temperature anisotropy and non-Maxwellian ion distributions associated with the fast flows on the ring current and the convection electric field.

Fast Solvers for Moving Material Interfaces

DTIC Science & Technology

2008-01-01

interface method—with the semi-Lagrangian contouring method developed in References [16–20]. We are now finalizing portable C / C ++ codes for fast adaptive ...stepping scheme couples a CIR predictor with a trapezoidal corrector using the velocity evaluated from the CIR approximation. It combines the...formula with efficient geometric algorithms and fast accurate contouring techniques. A modular adaptive implementation with fast new geometry modules

fast_protein_cluster: parallel and optimized clustering of large-scale protein modeling data.

PubMed

Hung, Ling-Hong; Samudrala, Ram

2014-06-15

fast_protein_cluster is a fast, parallel and memory efficient package used to cluster 60 000 sets of protein models (with up to 550 000 models per set) generated by the Nutritious Rice for the World project. fast_protein_cluster is an optimized and extensible toolkit that supports Root Mean Square Deviation after optimal superposition (RMSD) and Template Modeling score (TM-score) as metrics. RMSD calculations using a laptop CPU are 60× faster than qcprot and 3× faster than current graphics processing unit (GPU) implementations. New GPU code further increases the speed of RMSD and TM-score calculations. fast_protein_cluster provides novel k-means and hierarchical clustering methods that are up to 250× and 2000× faster, respectively, than Clusco, and identify significantly more accurate models than Spicker and Clusco. fast_protein_cluster is written in C++ using OpenMP for multi-threading support. Custom streaming Single Instruction Multiple Data (SIMD) extensions and advanced vector extension intrinsics code accelerate CPU calculations, and OpenCL kernels support AMD and Nvidia GPUs. fast_protein_cluster is available under the M.I.T. license. (http://software.compbio.washington.edu/fast_protein_cluster) © The Author 2014. Published by Oxford University Press.

Leap Frog and Time Step Sub-Cycle Scheme for Coupled Neutronics and Thermal-Hydraulic Codes

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

Lu, S.

2002-07-01

As the result of the advancing TCP/IP based inter-process communication technology, more and more legacy thermal-hydraulic codes have been coupled with neutronics codes to provide best-estimate capabilities for reactivity related reactor transient analysis. Most of the coupling schemes are based on closely coupled serial or parallel approaches. Therefore, the execution of the coupled codes usually requires significant CPU time, when a complicated system is analyzed. Leap Frog scheme has been used to reduce the run time. The extent of the decoupling is usually determined based on a trial and error process for a specific analysis. It is the intent ofmore » this paper to develop a set of general criteria, which can be used to invoke the automatic Leap Frog algorithm. The algorithm will not only provide the run time reduction but also preserve the accuracy. The criteria will also serve as the base of an automatic time step sub-cycle scheme when a sudden reactivity change is introduced and the thermal-hydraulic code is marching with a relatively large time step. (authors)« less

Software user's guide for determining the Pennsylvania scour critical indicator code and streambed scour assessment rating for roadway bridges

USGS Publications Warehouse

Henneberg, M.F.; Strause, J.L.

2002-01-01

This report presents the instructions required to use the Scour Critical Bridge Indicator (SCBI) Code and Scour Assessment Rating (SAR) calculator developed by the Pennsylvania Department of Transportation (PennDOT) and the U.S. Geological Survey to identify Pennsylvania bridges with excessive scour conditions or a high potential for scour. Use of the calculator will enable PennDOT bridge personnel to quickly calculate these scour indices if site conditions change, new bridges are constructed, or new information needs to be included. Both indices are calculated for a bridge simultaneously because they must be used together to be interpreted accurately. The SCBI Code and SAR calculator program is run by a World Wide Web browser from a remote computer. The user can 1) add additional scenarios for bridges in the SCBI Code and SAR calculator database or 2) enter data for new bridges and run the program to calculate the SCBI Code and calculate the SAR. The calculator program allows the user to print the results and to save multiple scenarios for a bridge.

A Secure and Robust Approach to Software Tamper Resistance

NASA Astrophysics Data System (ADS)

Ghosh, Sudeep; Hiser, Jason D.; Davidson, Jack W.

Software tamper-resistance mechanisms have increasingly assumed significance as a technique to prevent unintended uses of software. Closely related to anti-tampering techniques are obfuscation techniques, which make code difficult to understand or analyze and therefore, challenging to modify meaningfully. This paper describes a secure and robust approach to software tamper resistance and obfuscation using process-level virtualization. The proposed techniques involve novel uses of software check summing guards and encryption to protect an application. In particular, a virtual machine (VM) is assembled with the application at software build time such that the application cannot run without the VM. The VM provides just-in-time decryption of the program and dynamism for the application's code. The application's code is used to protect the VM to ensure a level of circular protection. Finally, to prevent the attacker from obtaining an analyzable snapshot of the code, the VM periodically discards all decrypted code. We describe a prototype implementation of these techniques and evaluate the run-time performance of applications using our system. We also discuss how our system provides stronger protection against tampering attacks than previously described tamper-resistance approaches.

The seasonal-cycle climate model

NASA Technical Reports Server (NTRS)

Marx, L.; Randall, D. A.

1981-01-01

The seasonal cycle run which will become the control run for the comparison with runs utilizing codes and parameterizations developed by outside investigators is discussed. The climate model currently exists in two parallel versions: one running on the Amdahl and the other running on the CYBER 203. These two versions are as nearly identical as machine capability and the requirement for high speed performance will allow. Developmental changes are made on the Amdahl/CMS version for ease of testing and rapidity of turnaround. The changes are subsequently incorporated into the CYBER 203 version using vectorization techniques where speed improvement can be realized. The 400 day seasonal cycle run serves as a control run for both medium and long range climate forecasts alsensitivity studies.

Rhexifolia versus Rhexiifolia: Plant Nomenclature Run Amok?

Treesearch

R. Kasten Dumroese; Mark W. Skinner

2005-01-01

The International Botanical Congress governs plant nomenclature worldwide through the International Code of Botanical Nomenclature. In the current code are very specific procedures for naming plants with novel compound epithets, and correcting compound epithets, like rhexifolia, that were incorrectly combined.We discuss why rhexiifolia...

Redistribution of Mechanical Work at the Knee and Ankle Joints During Fast Running in Minimalist Shoes

PubMed Central

Fuller, Joel T.; Buckley, Jonathan D.; Tsiros, Margarita D.; Brown, Nicholas A. T.; Thewlis, Dominic

2016-01-01

Context: Minimalist shoes have been suggested as a way to alter running biomechanics to improve running performance and reduce injuries. However, to date, researchers have only considered the effect of minimalist shoes at slow running speeds. Objective: To determine if runners change foot-strike pattern and alter the distribution of mechanical work at the knee and ankle joints when running at a fast speed in minimalist shoes compared with conventional running shoes. Design: Crossover study. Setting: Research laboratory. Patients or Other Participants: Twenty-six trained runners (age = 30.0 ± 7.9 years [age range, 18−40 years], height = 1.79 ± 0.06 m, mass = 75.3 ± 8.2 kg, weekly training distance = 27 ± 15 km) who ran with a habitual rearfoot foot-strike pattern and had no experience running in minimalist shoes. Intervention(s): Participants completed overground running trials at 18 km/h in minimalist and conventional shoes. Main Outcome Measure(s): Sagittal-plane kinematics and joint work at the knee and ankle joints were computed using 3-dimensional kinematic and ground reaction force data. Foot-strike pattern was classified as rearfoot, midfoot, or forefoot strike based on strike index and ankle angle at initial contact. Results: We observed no difference in foot-strike classification between shoes (χ21 = 2.29, P = .13). Ankle angle at initial contact was less (2.46° versus 7.43°; t25 = 3.34, P = .003) and strike index was greater (35.97% versus 29.04%; t25 = 2.38, P = .03) when running in minimalist shoes compared with conventional shoes. We observed greater negative (52.87 J versus 42.46 J; t24 = 2.29, P = .03) and positive work (68.91 J versus 59.08 J; t24 = 2.65, P = .01) at the ankle but less negative (59.01 J versus 67.02 J; t24 = 2.25, P = .03) and positive work (40.37 J versus 47.09 J; t24 = 2.11, P = .046) at the knee with minimalist shoes compared with conventional shoes. Conclusions: Running in minimalist shoes at a fast speed caused a redistribution of work from the knee to the ankle joint. This finding suggests that runners changing from conventional to minimalist shoes for short-distance races could be at an increased risk of ankle and calf injuries but a reduced risk of knee injuries. PMID:27834504

Achieving behavioral control with millisecond resolution in a high-level programming environment.

PubMed

Asaad, Wael F; Eskandar, Emad N

2008-08-30

The creation of psychophysical tasks for the behavioral neurosciences has generally relied upon low-level software running on a limited range of hardware. Despite the availability of software that allows the coding of behavioral tasks in high-level programming environments, many researchers are still reluctant to trust the temporal accuracy and resolution of programs running in such environments, especially when they run atop non-real-time operating systems. Thus, the creation of behavioral paradigms has been slowed by the intricacy of the coding required and their dissemination across labs has been hampered by the various types of hardware needed. However, we demonstrate here that, when proper measures are taken to handle the various sources of temporal error, accuracy can be achieved at the 1 ms time-scale that is relevant for the alignment of behavioral and neural events.

Fast and efficient compression of floating-point data.

PubMed

Lindstrom, Peter; Isenburg, Martin

2006-01-01

Large scale scientific simulation codes typically run on a cluster of CPUs that write/read time steps to/from a single file system. As data sets are constantly growing in size, this increasingly leads to I/O bottlenecks. When the rate at which data is produced exceeds the available I/O bandwidth, the simulation stalls and the CPUs are idle. Data compression can alleviate this problem by using some CPU cycles to reduce the amount of data needed to be transfered. Most compression schemes, however, are designed to operate offline and seek to maximize compression, not throughput. Furthermore, they often require quantizing floating-point values onto a uniform integer grid, which disqualifies their use in applications where exact values must be retained. We propose a simple scheme for lossless, online compression of floating-point data that transparently integrates into the I/O of many applications. A plug-in scheme for data-dependent prediction makes our scheme applicable to a wide variety of data used in visualization, such as unstructured meshes, point sets, images, and voxel grids. We achieve state-of-the-art compression rates and speeds, the latter in part due to an improved entropy coder. We demonstrate that this significantly accelerates I/O throughput in real simulation runs. Unlike previous schemes, our method also adapts well to variable-precision floating-point and integer data.

An electrocorticographic BCI using code-based VEP for control in video applications: a single-subject study

PubMed Central

Kapeller, Christoph; Kamada, Kyousuke; Ogawa, Hiroshi; Prueckl, Robert; Scharinger, Josef; Guger, Christoph

2014-01-01

A brain-computer-interface (BCI) allows the user to control a device or software with brain activity. Many BCIs rely on visual stimuli with constant stimulation cycles that elicit steady-state visual evoked potentials (SSVEP) in the electroencephalogram (EEG). This EEG response can be generated with a LED or a computer screen flashing at a constant frequency, and similar EEG activity can be elicited with pseudo-random stimulation sequences on a screen (code-based BCI). Using electrocorticography (ECoG) instead of EEG promises higher spatial and temporal resolution and leads to more dominant evoked potentials due to visual stimulation. This work is focused on BCIs based on visual evoked potentials (VEP) and its capability as a continuous control interface for augmentation of video applications. One 35 year old female subject with implanted subdural grids participated in the study. The task was to select one out of four visual targets, while each was flickering with a code sequence. After a calibration run including 200 code sequences, a linear classifier was used during an evaluation run to identify the selected visual target based on the generated code-based VEPs over 20 trials. Multiple ECoG buffer lengths were tested and the subject reached a mean online classification accuracy of 99.21% for a window length of 3.15 s. Finally, the subject performed an unsupervised free run in combination with visual feedback of the current selection. Additionally, an algorithm was implemented that allowed to suppress false positive selections and this allowed the subject to start and stop the BCI at any time. The code-based BCI system attained very high online accuracy, which makes this approach very promising for control applications where a continuous control signal is needed. PMID:25147509

3D unstructured-mesh radiation transport codes

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

Morel, J.

1997-12-31

Three unstructured-mesh radiation transport codes are currently being developed at Los Alamos National Laboratory. The first code is ATTILA, which uses an unstructured tetrahedral mesh in conjunction with standard Sn (discrete-ordinates) angular discretization, standard multigroup energy discretization, and linear-discontinuous spatial differencing. ATTILA solves the standard first-order form of the transport equation using source iteration in conjunction with diffusion-synthetic acceleration of the within-group source iterations. DANTE is designed to run primarily on workstations. The second code is DANTE, which uses a hybrid finite-element mesh consisting of arbitrary combinations of hexahedra, wedges, pyramids, and tetrahedra. DANTE solves several second-order self-adjoint forms of the transport equation including the even-parity equation, the odd-parity equation, and a new equation called the self-adjoint angular flux equation. DANTE also offers three angular discretization options:more » $$S{_}n$$ (discrete-ordinates), $$P{_}n$$ (spherical harmonics), and $$SP{_}n$$ (simplified spherical harmonics). DANTE is designed to run primarily on massively parallel message-passing machines, such as the ASCI-Blue machines at LANL and LLNL. The third code is PERICLES, which uses the same hybrid finite-element mesh as DANTE, but solves the standard first-order form of the transport equation rather than a second-order self-adjoint form. DANTE uses a standard $$S{_}n$$ discretization in angle in conjunction with trilinear-discontinuous spatial differencing, and diffusion-synthetic acceleration of the within-group source iterations. PERICLES was initially designed to run on workstations, but a version for massively parallel message-passing machines will be built. The three codes will be described in detail and computational results will be presented.« less

Modeling and Analysis of Actinide Diffusion Behavior in Irradiated Metal Fuel

NASA Astrophysics Data System (ADS)

Edelmann, Paul G.

There have been numerous attempts to model fast reactor fuel behavior in the last 40 years. The US currently does not have a fully reliable tool to simulate the behavior of metal fuels in fast reactors. The experimental database necessary to validate the codes is also very limited. The DOE-sponsored Advanced Fuels Campaign (AFC) has performed various experiments that are ready for analysis. Current metal fuel performance codes are either not available to the AFC or have limitations and deficiencies in predicting AFC fuel performance. A modified version of a new fuel performance code, FEAST-Metal , was employed in this investigation with useful results. This work explores the modeling and analysis of AFC metallic fuels using FEAST-Metal, particularly in the area of constituent actinide diffusion behavior. The FEAST-Metal code calculations for this work were conducted at Los Alamos National Laboratory (LANL) in support of on-going activities related to sensitivity analysis of fuel performance codes. A sensitivity analysis of FEAST-Metal was completed to identify important macroscopic parameters of interest to modeling and simulation of metallic fuel performance. A modification was made to the FEAST-Metal constituent redistribution model to enable accommodation of newer AFC metal fuel compositions with verified results. Applicability of this modified model for sodium fast reactor metal fuel design is demonstrated.

Positive Selection Underlies Faster-Z Evolution of Gene Expression in Birds.

PubMed

Dean, Rebecca; Harrison, Peter W; Wright, Alison E; Zimmer, Fabian; Mank, Judith E

2015-10-01

The elevated rate of evolution for genes on sex chromosomes compared with autosomes (Fast-X or Fast-Z evolution) can result either from positive selection in the heterogametic sex or from nonadaptive consequences of reduced relative effective population size. Recent work in birds suggests that Fast-Z of coding sequence is primarily due to relaxed purifying selection resulting from reduced relative effective population size. However, gene sequence and gene expression are often subject to distinct evolutionary pressures; therefore, we tested for Fast-Z in gene expression using next-generation RNA-sequencing data from multiple avian species. Similar to studies of Fast-Z in coding sequence, we recover clear signatures of Fast-Z in gene expression; however, in contrast to coding sequence, our data indicate that Fast-Z in expression is due to positive selection acting primarily in females. In the soma, where gene expression is highly correlated between the sexes, we detected Fast-Z in both sexes, although at a higher rate in females, suggesting that many positively selected expression changes in females are also expressed in males. In the gonad, where intersexual correlations in expression are much lower, we detected Fast-Z for female gene expression, but crucially, not males. This suggests that a large amount of expression variation is sex-specific in its effects within the gonad. Taken together, our results indicate that Fast-Z evolution of gene expression is the product of positive selection acting on recessive beneficial alleles in the heterogametic sex. More broadly, our analysis suggests that the adaptive potential of Z chromosome gene expression may be much greater than that of gene sequence, results which have important implications for the role of sex chromosomes in speciation and sexual selection. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Applications of Coding in Network Communications

ERIC Educational Resources Information Center

Chang, Christopher SungWook

2012-01-01

This thesis uses the tool of network coding to investigate fast peer-to-peer file distribution, anonymous communication, robust network construction under uncertainty, and prioritized transmission. In a peer-to-peer file distribution system, we use a linear optimization approach to show that the network coding framework significantly simplifies…

Fluidica CFD software for fluids instruction

NASA Astrophysics Data System (ADS)

Colonius, Tim

2008-11-01

Fluidica is an open-source freely available Matlab graphical user interface (GUI) to to an immersed-boundary Navier- Stokes solver. The algorithm is programmed in Fortran and compiled into Matlab as mex-function. The user can create external flows about arbitrarily complex bodies and collections of free vortices. The code runs fast enough for complex 2D flows to be computed and visualized in real-time on the screen. This facilitates its use in homework and in the classroom for demonstrations of various potential-flow and viscous flow phenomena. The GUI has been written with the goal of allowing the student to learn how to use the software as she goes along. The user can select which quantities are viewed on the screen, including contours of various scalars, velocity vectors, streamlines, particle trajectories, streaklines, and finite-time Lyapunov exponents. In this talk, we demonstrate the software in the context of worked classroom examples demonstrating lift and drag, starting vortices, separation, and vortex dynamics.

Block-Parallel Data Analysis with DIY2

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

Morozov, Dmitriy; Peterka, Tom

DIY2 is a programming model and runtime for block-parallel analytics on distributed-memory machines. Its main abstraction is block-structured data parallelism: data are decomposed into blocks; blocks are assigned to processing elements (processes or threads); computation is described as iterations over these blocks, and communication between blocks is defined by reusable patterns. By expressing computation in this general form, the DIY2 runtime is free to optimize the movement of blocks between slow and fast memories (disk and flash vs. DRAM) and to concurrently execute blocks residing in memory with multiple threads. This enables the same program to execute in-core, out-of-core, serial,more » parallel, single-threaded, multithreaded, or combinations thereof. This paper describes the implementation of the main features of the DIY2 programming model and optimizations to improve performance. DIY2 is evaluated on benchmark test cases to establish baseline performance for several common patterns and on larger complete analysis codes running on large-scale HPC machines.« less

Fast and sensitive taxonomic classification for metagenomics with Kaiju

PubMed Central

Menzel, Peter; Ng, Kim Lee; Krogh, Anders

2016-01-01

Metagenomics emerged as an important field of research not only in microbial ecology but also for human health and disease, and metagenomic studies are performed on increasingly larger scales. While recent taxonomic classification programs achieve high speed by comparing genomic k-mers, they often lack sensitivity for overcoming evolutionary divergence, so that large fractions of the metagenomic reads remain unclassified. Here we present the novel metagenome classifier Kaiju, which finds maximum (in-)exact matches on the protein-level using the Burrows–Wheeler transform. We show in a genome exclusion benchmark that Kaiju classifies reads with higher sensitivity and similar precision compared with current k-mer-based classifiers, especially in genera that are underrepresented in reference databases. We also demonstrate that Kaiju classifies up to 10 times more reads in real metagenomes. Kaiju can process millions of reads per minute and can run on a standard PC. Source code and web server are available at http://kaiju.binf.ku.dk. PMID:27071849

Fast and sensitive taxonomic classification for metagenomics with Kaiju.

PubMed

Menzel, Peter; Ng, Kim Lee; Krogh, Anders

2016-04-13

Metagenomics emerged as an important field of research not only in microbial ecology but also for human health and disease, and metagenomic studies are performed on increasingly larger scales. While recent taxonomic classification programs achieve high speed by comparing genomic k-mers, they often lack sensitivity for overcoming evolutionary divergence, so that large fractions of the metagenomic reads remain unclassified. Here we present the novel metagenome classifier Kaiju, which finds maximum (in-)exact matches on the protein-level using the Burrows-Wheeler transform. We show in a genome exclusion benchmark that Kaiju classifies reads with higher sensitivity and similar precision compared with current k-mer-based classifiers, especially in genera that are underrepresented in reference databases. We also demonstrate that Kaiju classifies up to 10 times more reads in real metagenomes. Kaiju can process millions of reads per minute and can run on a standard PC. Source code and web server are available at http://kaiju.binf.ku.dk.

Alternate Operating Modes For NDCX-II

NASA Astrophysics Data System (ADS)

Sharp, W. M.; Friedman, A.; Grote, D. P.; Cohen, R. H.; Lund, S. M.; Vay, J.-L.; Waldron, W. L.

2012-10-01

NDCX-II is a newly completed accelerator facility at LBNL, built to study ion-heated warm dense matter and aspects of ion-driven targets for inertial-fusion energy. The baseline design calls for using twelve induction cells to accelerate 40 nC of Li+ ions to 1.2 MeV. During commissioning, though, we plan to extend the source lifetime by extracting less total charge. For operational flexibility, the option of using a helium plasma source is also being investigated. Over time, we expect that NDCX-II will be upgraded to substantially higher energies, necessitating the use of heavier ions to keep a suitable deposition range in targets. Each of these options requires development of an alternate acceleration schedule and the associated transverse focusing. The schedules here are first worked out with a fast-running 1-D particle-in-cell code ASP, then 2-D and 3-D Warp simulations are used to verify the 1-D results and to design transverse focusing.

Loss-of-flow-without-scram tests in Experimental Breeder Reactor-II and comparison with pretest predictions

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

Chang, L.K.; Mohr, D.; Planchon, H.P.

This article discusses a series of successful loss-of-flow-without-scram tests conducted in Experimental Breeder Reactor-II (EBR-II), a metal-fueled, sodium-cooled fast reactor. These May 1985 tests demonstrated the capability of the EBR to reduce reactor power passively during a loss of flow and to maintain reactor temperatures within bounds without any reliance on an active safety system. The tests were run from reduced power to ensure that temperatures could be maintained well below the fuel-clad eutectic temperature. Good agreement was found between selected test data and pretest predictions made with the EBR-II system analysis code NATDEMO and the hot channel analysis codemore » HOTCHAN. The article also discusses safety assessments of the tests as well as modifications required on the EBR-II reactor safety system for conducting required on the EBR-II reactor safety system for the conducting the tests.« less

Oak Ridge National Laboratory Support of Non-light Water Reactor Technologies: Capabilities Assessment for NRC Near-term Implementation Action Plans for Non-light Water Reactors

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

Belles, Randy; Jain, Prashant K.; Powers, Jeffrey J.

The Oak Ridge National Laboratory (ORNL) has a rich history of support for light water reactor (LWR) and non-LWR technologies. The ORNL history involves operation of 13 reactors at ORNL including the graphite reactor dating back to World War II, two aqueous homogeneous reactors, two molten salt reactors (MSRs), a fast-burst health physics reactor, and seven LWRs. Operation of the High Flux Isotope Reactor (HFIR) has been ongoing since 1965. Expertise exists amongst the ORNL staff to provide non-LWR training; support evaluation of non-LWR licensing and safety issues; perform modeling and simulation using advanced computational tools; run laboratory experiments usingmore » equipment such as the liquid salt component test facility; and perform in-depth fuel performance and thermal-hydraulic technology reviews using a vast suite of computer codes and tools. Summaries of this expertise are included in this paper.« less

A fast parallel clustering algorithm for molecular simulation trajectories.

PubMed

Zhao, Yutong; Sheong, Fu Kit; Sun, Jian; Sander, Pedro; Huang, Xuhui

2013-01-15

We implemented a GPU-powered parallel k-centers algorithm to perform clustering on the conformations of molecular dynamics (MD) simulations. The algorithm is up to two orders of magnitude faster than the CPU implementation. We tested our algorithm on four protein MD simulation datasets ranging from the small Alanine Dipeptide to a 370-residue Maltose Binding Protein (MBP). It is capable of grouping 250,000 conformations of the MBP into 4000 clusters within 40 seconds. To achieve this, we effectively parallelized the code on the GPU and utilize the triangle inequality of metric spaces. Furthermore, the algorithm's running time is linear with respect to the number of cluster centers. In addition, we found the triangle inequality to be less effective in higher dimensions and provide a mathematical rationale. Finally, using Alanine Dipeptide as an example, we show a strong correlation between cluster populations resulting from the k-centers algorithm and the underlying density. © 2012 Wiley Periodicals, Inc. Copyright © 2012 Wiley Periodicals, Inc.

The Impact of Odor--Reward Memory on Chemotaxis in Larval "Drosophila"

ERIC Educational Resources Information Center

Schleyer, Michael; Reid, Samuel F.; Pamir, Evren; Saumweber, Timo; Paisios, Emmanouil; Davies, Alexander; Gerber, Bertram; Louis, Matthieu

2015-01-01

How do animals adaptively integrate innate with learned behavioral tendencies? We tackle this question using chemotaxis as a paradigm. Chemotaxis in the "Drosophila" larva largely results from a sequence of runs and oriented turns. Thus, the larvae minimally need to determine (i) how fast to run, (ii) when to initiate a turn, and (iii)…

The Red Queen Visits Minkowski Space

ERIC Educational Resources Information Center

Low, Robert J.

2007-01-01

When Alice went "Through the Looking Glass", she found herself in a situation where she had to run as fast as she could in order to stay still. In accordance with the dictum that truth is stranger than fiction, we will see that it is possible to find a situation in special relativity where running towards one's target is actually…

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.

Mapping and DOWNFLOW simulation of recent lava flow fields at Mount Etna

NASA Astrophysics Data System (ADS)

Tarquini, Simone; Favalli, Massimiliano

2011-07-01

In recent years, progress in geographic information systems (GIS) and remote sensing techniques have allowed the mapping and studying of lava flows in unprecedented detail. A composite GIS technique is introduced to obtain high resolution boundaries of lava flow fields. This technique is mainly based on the processing of LIDAR-derived maps and digital elevation models (DEMs). The probabilistic code DOWNFLOW is then used to simulate eight large flow fields formed at Mount Etna in the last 25 years. Thanks to the collection of 6 DEMs representing Mount Etna at different times from 1986 to 2007, simulated outputs are obtained by running the DOWNFLOW code over pre-emplacement topographies. Simulation outputs are compared with the boundaries of the actual flow fields obtained here or derived from the existing literature. Although the selected fields formed in accordance with different emplacement mechanisms, flowed on different zones of the volcano over different topographies and were fed by different lava supplies of different durations, DOWNFLOW yields results close to the actual flow fields in all the cases considered. This outcome is noteworthy because DOWNFLOW has been applied by adopting a default calibration, without any specific tuning for the new cases considered here. This extensive testing proves that, if the pre-emplacement topography is available, DOWNFLOW yields a realistic simulation of a future lava flow based solely on a knowledge of the vent position. In comparison with deterministic codes, which require accurate knowledge of a large number of input parameters, DOWNFLOW turns out to be simple, fast and undemanding, proving to be ideal for systematic hazard and risk analyses.

Distributed multitasking ITS with PVM

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

Fan, W.C.; Halbleib, J.A. Sr.

1995-12-31

Advances in computer hardware and communication software have made it possible to perform parallel-processing computing on a collection of desktop workstations. For many applications, multitasking on a cluster of high-performance workstations has achieved performance comparable to or better than that on a traditional supercomputer. From the point of view of cost-effectiveness, it also allows users to exploit available but unused computational resources and thus achieve a higher performance-to-cost ratio. Monte Carlo calculations are inherently parallelizable because the individual particle trajectories can be generated independently with minimum need for interprocessor communication. Furthermore, the number of particle histories that can be generatedmore » in a given amount of wall-clock time is nearly proportional to the number of processors in the cluster. This is an important fact because the inherent statistical uncertainty in any Monte Carlo result decreases as the number of histories increases. For these reasons, researchers have expended considerable effort to take advantage of different parallel architectures for a variety of Monte Carlo radiation transport codes, often with excellent results. The initial interest in this work was sparked by the multitasking capability of the MCNP code on a cluster of workstations using the Parallel Virtual Machine (PVM) software. On a 16-machine IBM RS/6000 cluster, it has been demonstrated that MCNP runs ten times as fast as on a single-processor CRAY YMP. In this paper, we summarize the implementation of a similar multitasking capability for the coupled electronphoton transport code system, the Integrated TIGER Series (ITS), and the evaluation of two load-balancing schemes for homogeneous and heterogeneous networks.« less

Knowledge Data Base for Amorphous Metals

DTIC Science & Technology

2007-07-26

not programmatic, updates. Over 100 custom SQL statements that maintain the domain specific data are attached to the workflow entries in a generic...for the form by populating the SQL and run generation tables. Application data may be prepared in different ways for two steps that invoke the same form...run generation mode). There is a single table of SQL commands. Each record has a user-definable ID, the SQL code, and a comment. The run generation

TABULATED EQUIVALENT SDR FLAMELET (TESF) MODEFL

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

KUNDU, PRITHWISH; AMEEN, mUHSIN MOHAMMED; UNNIKRISHNAN, UMESH

The code consists of an implementation of a novel tabulated combustion model for non-premixed flames in CFD solvers. This novel technique/model is used to implement an unsteady flamelet tabulation without using progress variables for non-premixed flames. It also has the capability to include history effects which is unique within tabulated flamelet models. The flamelet table generation code can be run in parallel to generate tables with large chemistry mechanisms in relatively short wall clock times. The combustion model/code reads these tables. This framework can be coupled with any CFD solver with RANS as well as LES turbulence models. This frameworkmore » enables CFD solvers to run large chemistry mechanisms with large number of grids at relatively lower computational costs. Currently it has been coupled with the Converge CFD code and validated against available experimental data. This model can be used to simulate non-premixed combustion in a variety of applications like reciprocating engines, gas turbines and industrial burners operating over a wide range of fuels.« less

xPerm: fast index canonicalization for tensor computer algebra

NASA Astrophysics Data System (ADS)

Martín-García, José M.

2008-10-01

We present a very fast implementation of the Butler-Portugal algorithm for index canonicalization with respect to permutation symmetries. It is called xPerm, and has been written as a combination of a Mathematica package and a C subroutine. The latter performs the most demanding parts of the computations and can be linked from any other program or computer algebra system. We demonstrate with tests and timings the effectively polynomial performance of the Butler-Portugal algorithm with respect to the number of indices, though we also show a case in which it is exponential. Our implementation handles generic tensorial expressions with several dozen indices in hundredths of a second, or one hundred indices in a few seconds, clearly outperforming all other current canonicalizers. The code has been already under intensive testing for several years and has been essential in recent investigations in large-scale tensor computer algebra. Program summaryProgram title: xPerm Catalogue identifier: AEBH_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEBH_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 93 582 No. of bytes in distributed program, including test data, etc.: 1 537 832 Distribution format: tar.gz Programming language: C and Mathematica (version 5.0 or higher) Computer: Any computer running C and Mathematica (version 5.0 or higher) Operating system: Linux, Unix, Windows XP, MacOS RAM:: 20 Mbyte Word size: 64 or 32 bits Classification: 1.5, 5 Nature of problem: Canonicalization of indexed expressions with respect to permutation symmetries. Solution method: The Butler-Portugal algorithm. Restrictions: Multiterm symmetries are not considered. Running time: A few seconds with generic expressions of up to 100 indices. The xPermDoc.nb notebook supplied with the distribution takes approximately one and a half hours to execute in full.

Underworld - Bringing a Research Code to the Classroom

NASA Astrophysics Data System (ADS)

Moresi, L. N.; Mansour, J.; Giordani, J.; Farrington, R.; Kaluza, O.; Quenette, S.; Woodcock, R.; Squire, G.

2017-12-01

While there are many reasons to celebrate the passing of punch card programming and flickering green screens,the loss of the sense of wonder at the very existence of computers and the calculations they make possible shouldnot be numbered among them. Computers have become so familiar that students are often unaware that formal and careful design of algorithms andtheir implementations remains a valuable and important skill that has to be learned and practiced to achieveexpertise and genuine understanding. In teaching geodynamics and geophysics at undergraduate level, we aimed to be able to bring our researchtools into the classroom - even when those tools are advanced, parallel research codes that we typically deploy on hundredsor thousands of processors, and we wanted to teach not just the physical concepts that are modelled by these codes but asense of familiarity with computational modelling and the ability to discriminate a reliable model from a poor one. The underworld code (www.underworldcode.org) was developed for modelling plate-scale fluid mechanics and studyingproblems in lithosphere dynamics. Though specialised for this task, underworld has a straightforwardpython user interface that allows it to run within the environment of jupyter notebooks on a laptop (at modest resolution, of course).The python interface was developed for adaptability in addressing new research problems, but also lends itself to integration intoa python-driven learning environment. To manage the heavy demands of installing and running underworld in a teaching laboratory, we have developed a workflow in whichwe install docker containers in the cloud which support a number of students to run their own environment independently. We share ourexperience blending notebooks and static webpages into a single web environment, and we explain how we designed our graphics andanalysis tools to allow notebook "scripts" to be queued and run on a supercomputer.

Limits to high-speed simulations of spiking neural networks using general-purpose computers.

PubMed

Zenke, Friedemann; Gerstner, Wulfram

2014-01-01

To understand how the central nervous system performs computations using recurrent neuronal circuitry, simulations have become an indispensable tool for theoretical neuroscience. To study neuronal circuits and their ability to self-organize, increasing attention has been directed toward synaptic plasticity. In particular spike-timing-dependent plasticity (STDP) creates specific demands for simulations of spiking neural networks. On the one hand a high temporal resolution is required to capture the millisecond timescale of typical STDP windows. On the other hand network simulations have to evolve over hours up to days, to capture the timescale of long-term plasticity. To do this efficiently, fast simulation speed is the crucial ingredient rather than large neuron numbers. Using different medium-sized network models consisting of several thousands of neurons and off-the-shelf hardware, we compare the simulation speed of the simulators: Brian, NEST and Neuron as well as our own simulator Auryn. Our results show that real-time simulations of different plastic network models are possible in parallel simulations in which numerical precision is not a primary concern. Even so, the speed-up margin of parallelism is limited and boosting simulation speeds beyond one tenth of real-time is difficult. By profiling simulation code we show that the run times of typical plastic network simulations encounter a hard boundary. This limit is partly due to latencies in the inter-process communications and thus cannot be overcome by increased parallelism. Overall, these results show that to study plasticity in medium-sized spiking neural networks, adequate simulation tools are readily available which run efficiently on small clusters. However, to run simulations substantially faster than real-time, special hardware is a prerequisite.

46 CFR 160.156-1 - Scope.

Code of Federal Regulations, 2012 CFR

2012-10-01

... APPROVAL LIFESAVING EQUIPMENT Rescue Boats and Fast Rescue Boats (SOLAS) § 160.156-1 Scope. This subpart... fast rescue boat, complying with SOLAS and the IMO LSA Code, for use on waters other than protected...

46 CFR 160.156-1 - Scope.

Code of Federal Regulations, 2013 CFR

2013-10-01

... APPROVAL LIFESAVING EQUIPMENT Rescue Boats and Fast Rescue Boats (SOLAS) § 160.156-1 Scope. This subpart... fast rescue boat, complying with SOLAS and the IMO LSA Code, for use on waters other than protected...

46 CFR 160.156-1 - Scope.

Code of Federal Regulations, 2014 CFR

2014-10-01

... APPROVAL LIFESAVING EQUIPMENT Rescue Boats and Fast Rescue Boats (SOLAS) § 160.156-1 Scope. This subpart... fast rescue boat, complying with SOLAS and the IMO LSA Code, for use on waters other than protected...

Development of Fast Algorithms Using Recursion, Nesting and Iterations for Computational Electromagnetics

NASA Technical Reports Server (NTRS)

Chew, W. C.; Song, J. M.; Lu, C. C.; Weedon, W. H.

1995-01-01

In the first phase of our work, we have concentrated on laying the foundation to develop fast algorithms, including the use of recursive structure like the recursive aggregate interaction matrix algorithm (RAIMA), the nested equivalence principle algorithm (NEPAL), the ray-propagation fast multipole algorithm (RPFMA), and the multi-level fast multipole algorithm (MLFMA). We have also investigated the use of curvilinear patches to build a basic method of moments code where these acceleration techniques can be used later. In the second phase, which is mainly reported on here, we have concentrated on implementing three-dimensional NEPAL on a massively parallel machine, the Connection Machine CM-5, and have been able to obtain some 3D scattering results. In order to understand the parallelization of codes on the Connection Machine, we have also studied the parallelization of 3D finite-difference time-domain (FDTD) code with PML material absorbing boundary condition (ABC). We found that simple algorithms like the FDTD with material ABC can be parallelized very well allowing us to solve within a minute a problem of over a million nodes. In addition, we have studied the use of the fast multipole method and the ray-propagation fast multipole algorithm to expedite matrix-vector multiplication in a conjugate-gradient solution to integral equations of scattering. We find that these methods are faster than LU decomposition for one incident angle, but are slower than LU decomposition when many incident angles are needed as in the monostatic RCS calculations.

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.

A novel bit-wise adaptable entropy coding technique

NASA Technical Reports Server (NTRS)

Kiely, A.; Klimesh, M.

2001-01-01

We present a novel entropy coding technique which is adaptable in that each bit to be encoded may have an associated probability esitmate which depends on previously encoded bits. The technique may have advantages over arithmetic coding. The technique can achieve arbitrarily small redundancy and admits a simple and fast decoder.

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.

Reliability assessment of MVP-BURN and JENDL-4.0 related to nuclear transmutation of light platinum group elements

NASA Astrophysics Data System (ADS)

Terashima, Atsunori; Nilsson, Mikael; Ozawa, Masaki; Chiba, Satoshi

2017-09-01

The Aprés ORIENT research program, as a concept of advanced nuclear fuel cycle, was initiated in FY2011 aiming at creating stable, highly-valuable elements by nuclear transmutation from ↓ssion products. In order to simulate creation of such elements by (n, γ) reaction succeeded by β- decay in reactors, a continuous-energy Monte Carlo burnup calculation code MVP-BURN was employed. Then, it is one of the most important tasks to con↓rm the reliability of MVP-BURN code and evaluated neutron cross section library. In this study, both an experiment of neutron activation analysis in TRIGA Mark I reactor at University of California, Irvine and the corresponding burnup calculation using MVP-BURN code were performed for validation of the simulation on transmutation of light platinum group elements. Especially, some neutron capture reactions such as 102Ru(n, γ)103Ru, 104Ru(n, γ)105Ru, and 108Pd(n, γ)109Pd were dealt with in this study. From a comparison between the calculation (C) and the experiment (E) about 102Ru(n, γ)103Ru, the deviation (C/E-1) was signi↓cantly large. Then, it is strongly suspected that not MVP-BURN code but the neutron capture cross section of 102Ru belonging to JENDL-4.0 used in this simulation have made the big di↑erence as (C/E-1) >20%.

A user's guide to Sandia's latin hypercube sampling software : LHS UNIX library/standalone version.

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

Swiler, Laura Painton; Wyss, Gregory Dane

2004-07-01

This document is a reference guide for the UNIX Library/Standalone version of the Latin Hypercube Sampling Software. This software has been developed to generate Latin hypercube multivariate samples. This version runs on Linux or UNIX platforms. This manual covers the use of the LHS code in a UNIX environment, run either as a standalone program or as a callable library. The underlying code in the UNIX Library/Standalone version of LHS is almost identical to the updated Windows version of LHS released in 1998 (SAND98-0210). However, some modifications were made to customize it for a UNIX environment and as a librarymore » that is called from the DAKOTA environment. This manual covers the use of the LHS code as a library and in the standalone mode under UNIX.« less

Comparison of SPHC Hydrocode Results with Penetration Equations and Results of Other Codes

NASA Technical Reports Server (NTRS)

Evans, Steven W.; Stallworth, Roderick; Stellingwerf, Robert F.

2004-01-01

The SPHC hydrodynamic code was used to simulate impacts of spherical aluminum projectiles on a single-wall aluminum plate and on a generic Whipple shield. Simulations were carried out in two and three dimensions. Projectile speeds ranged from 2 kilometers per second to 10 kilometers per second for the single-wall runs, and from 3 kilometers per second to 40 kilometers per second for the Whipple shield runs. Spallation limit results of the single-wall simulations are compared with predictions from five standard penetration equations, and are shown to fall comfortably within the envelope of these analytical relations. Ballistic limit results of the Whipple shield simulations are compared with results from the AUTODYN-2D and PAM-SHOCK-3D codes presented in a paper at the Hypervelocity Impact Symposium 2000 and the Christiansen formulation of 2003.

Syndrome-source-coding and its universal generalization. [error correcting codes for data compression

NASA Technical Reports Server (NTRS)

Ancheta, T. C., Jr.

1976-01-01

A method of using error-correcting codes to obtain data compression, called syndrome-source-coding, is described in which the source sequence is treated as an error pattern whose syndrome forms the compressed data. It is shown that syndrome-source-coding can achieve arbitrarily small distortion with the number of compressed digits per source digit arbitrarily close to the entropy of a binary memoryless source. A 'universal' generalization of syndrome-source-coding is formulated which provides robustly effective distortionless coding of source ensembles. Two examples are given, comparing the performance of noiseless universal syndrome-source-coding to (1) run-length coding and (2) Lynch-Davisson-Schalkwijk-Cover universal coding for an ensemble of binary memoryless sources.

Fast running restricts evolutionary change of the vertebral column in mammals

PubMed Central

Galis, Frietson; Carrier, David R.; van Alphen, Joris; van der Mije, Steven D.; Van Dooren, Tom J. M.; Metz, Johan A. J.; ten Broek, Clara M. A.

2014-01-01

The mammalian vertebral column is highly variable, reflecting adaptations to a wide range of lifestyles, from burrowing in moles to flying in bats. However, in many taxa, the number of trunk vertebrae is surprisingly constant. We argue that this constancy results from strong selection against initial changes of these numbers in fast running and agile mammals, whereas such selection is weak in slower-running, sturdier mammals. The rationale is that changes of the number of trunk vertebrae require homeotic transformations from trunk into sacral vertebrae, or vice versa, and mutations toward such transformations generally produce transitional lumbosacral vertebrae that are incompletely fused to the sacrum. We hypothesize that such incomplete homeotic transformations impair flexibility of the lumbosacral joint and thereby threaten survival in species that depend on axial mobility for speed and agility. Such transformations will only marginally affect performance in slow, sturdy species, so that sufficient individuals with transitional vertebrae survive to allow eventual evolutionary changes of trunk vertebral numbers. We present data on fast and slow carnivores and artiodactyls and on slow afrotherians and monotremes that strongly support this hypothesis. The conclusion is that the selective constraints on the count of trunk vertebrae stem from a combination of developmental and biomechanical constraints. PMID:25024205

Automated Detection and Analysis of Interplanetary Shocks Running Real-Time on the Web

NASA Astrophysics Data System (ADS)

Vorotnikov, V.; Smith, C. W.; Hu, Q.; Szabo, A.; Skoug, R. M.; Cohen, C. M.; Davis, A. J.

2008-05-01

The ACE real-time data stream provides web-based now-casting capabilities for solar wind conditions upstream of Earth. We have built a fully automated code that finds and analyzes interplanetary shocks as they occur and posts their solutions on the Web for possible real-time application to space weather nowcasting. Shock analysis algorithms based on the Rankine-Hugoniot jump conditions exist and are in wide-spread use today for the interactive analysis of interplanetary shocks yielding parameters such as shock speed and propagation direction and shock strength in the form of compression ratios. At a previous meeting we reported on efforts to develop a fully automated code that used ACE Level-2 (science quality) data to prove the applicability and correctness of the code and the associated shock-finder. We have since adapted the code to run ACE RTSW data provided by NOAA. This data lacks the full 3-dimensional velocity vector for the solar wind and contains only a single component wind speed. We show that by assuming the wind velocity to be radial strong shock solutions remain essentially unchanged and the analysis performs as well as it would if 3-D velocity components were available. This is due, at least in part, to the fact that strong shocks tend to have nearly radial shock normals and it is the strong shocks that are most effective in space weather applications. Strong shocks are the only shocks that concern us in this application. The code is now running on the Web and the results are available to all.

Fast Model Generalized Pseudopotential Theory Interatomic Potential Routine

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

2015-03-18

MGPT is an unclassified source code for the fast evaluation and application of quantum-based MGPT interatomic potentials for mrtals. The present version of MGPT has been developed entirely at LLNL, but is specifically designed for implementation in the open-source molecular0dynamics code LAMMPS maintained by Sandia National Laboratories. Using MGPT in LAMMPS, with separate input potential data, one can perform large-scale atomistic simulations of the structural, thermodynamic, defeat and mechanical properties of transition metals with quantum-mechanical realism.

Subscale Fast Cookoff Testing and Modeling for the Hazard Assessment of Large Rocket Motors

DTIC Science & Technology

2001-03-01

41 LIST OF TABLES Table 1 Heats of Vaporization Parameter for Two-liner Phase Transformation - Complete Liner Sublimation and/or Combined Liner...One-dimensional 2-D Two-dimensional ALE3D Arbitrary-Lagrange-Eulerian (3-D) Computer Code ALEGRA 3-D Arbitrary-Lagrange-Eulerian Computer Code for...case-liner bond areas and in the grain inner bore to explore the pre-ignition and ignition phases , as well as burning evolution in rocket motor fast

Singer product apertures-A coded aperture system with a fast decoding algorithm

NASA Astrophysics Data System (ADS)

Byard, Kevin; Shutler, Paul M. E.

2017-06-01

A new type of coded aperture configuration that enables fast decoding of the coded aperture shadowgram data is presented. Based on the products of incidence vectors generated from the Singer difference sets, we call these Singer product apertures. For a range of aperture dimensions, we compare experimentally the performance of three decoding methods: standard decoding, induction decoding and direct vector decoding. In all cases the induction and direct vector methods are several orders of magnitude faster than the standard method, with direct vector decoding being significantly faster than induction decoding. For apertures of the same dimensions the increase in speed offered by direct vector decoding over induction decoding is better for lower throughput apertures.

Benchmarking study of the MCNP code against cold critical experiments

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

Sitaraman, S.

1991-01-01

The purpose of this study was to benchmark the widely used Monte Carlo code MCNP against a set of cold critical experiments with a view to using the code as a means of independently verifying the performance of faster but less accurate Monte Carlo and deterministic codes. The experiments simulated consisted of both fast and thermal criticals as well as fuel in a variety of chemical forms. A standard set of benchmark cold critical experiments was modeled. These included the two fast experiments, GODIVA and JEZEBEL, the TRX metallic uranium thermal experiments, the Babcock and Wilcox oxide and mixed oxidemore » experiments, and the Oak Ridge National Laboratory (ORNL) and Pacific Northwest Laboratory (PNL) nitrate solution experiments. The principal case studied was a small critical experiment that was performed with boiling water reactor bundles.« less

Building 1D resonance broadened quasilinear (RBQ) code for fast ions Alfvénic relaxations

NASA Astrophysics Data System (ADS)

Gorelenkov, Nikolai; Duarte, Vinicius; Berk, Herbert

2016-10-01

The performance of the burning plasma is limited by the confinement of superalfvenic fusion products, e.g. alpha particles, which are capable of resonating with the Alfvénic eigenmodes (AEs). The effect of AEs on fast ions is evaluated using a resonance line broadened diffusion coefficient. The interaction of fast ions and AEs is captured for cases where there are either isolated or overlapping modes. A new code RBQ1D is being built which constructs diffusion coefficients based on realistic eigenfunctions that are determined by the ideal MHD code NOVA. The wave particle interaction can be reduced to one-dimensional dynamics where for the Alfvénic modes typically the particle kinetic energy is nearly constant. Hence to a good approximation the Quasi-Linear (QL) diffusion equation only contains derivatives in the angular momentum. The diffusion equation is then one dimensional that is efficiently solved simultaneously for all particles with the equation for the evolution of the wave angular momentum. The evolution of fast ion constants of motion is governed by the QL diffusion equations which are adapted to find the ion distribution function.

On FAST3D simulations of directly-driven inertial-fusion targets with high-Z layers for reducing laser imprint and surface non-uniformity growth

NASA Astrophysics Data System (ADS)

Bates, Jason; Schmitt, Andrew; Klapisch, Marcel; Karasik, Max; Obenschain, Steve

2013-10-01

Modifications to the FAST3D code have been made to enhance its ability to simulate the dynamics of plastic ICF targets with high-Z overcoats. This class of problems is challenging computationally due in part to plasma conditions that are not in a state of local thermodynamic equilibrium and to the presence of mixed computational cells containing more than one material. Recently, new opacity tables for gold, palladium and plastic have been generated with an improved version of the STA code. These improved tables provide smoother, higher-fidelity opacity data over a wider range of temperature and density states than before, and contribute to a more accurate treatment of radiative transfer processes in FAST3D simulations. Furthermore, a new, more efficient subroutine known as ``MMEOS'' has been installed in the FAST3D code for determining pressure and temperature equilibrium conditions within cells containing multiple materials. We will discuss these topics, and present new simulation results for high-Z planar-target experiments performed recently on the NIKE Laser Facility. Work supported by DOE/NNSA.

SGO: A fast engine for ab initio atomic structure global optimization by differential evolution

NASA Astrophysics Data System (ADS)

Chen, Zhanghui; Jia, Weile; Jiang, Xiangwei; Li, Shu-Shen; Wang, Lin-Wang

2017-10-01

As the high throughout calculations and material genome approaches become more and more popular in material science, the search for optimal ways to predict atomic global minimum structure is a high research priority. This paper presents a fast method for global search of atomic structures at ab initio level. The structures global optimization (SGO) engine consists of a high-efficiency differential evolution algorithm, accelerated local relaxation methods and a plane-wave density functional theory code running on GPU machines. The purpose is to show what can be achieved by combining the superior algorithms at the different levels of the searching scheme. SGO can search the global-minimum configurations of crystals, two-dimensional materials and quantum clusters without prior symmetry restriction in a relatively short time (half or several hours for systems with less than 25 atoms), thus making such a task a routine calculation. Comparisons with other existing methods such as minima hopping and genetic algorithm are provided. One motivation of our study is to investigate the properties of magnetic systems in different phases. The SGO engine is capable of surveying the local minima surrounding the global minimum, which provides the information for the overall energy landscape of a given system. Using this capability we have found several new configurations for testing systems, explored their energy landscape, and demonstrated that the magnetic moment of metal clusters fluctuates strongly in different local minima.

Particle In Cell Codes on Highly Parallel Architectures

NASA Astrophysics Data System (ADS)

Tableman, Adam

2014-10-01

We describe strategies and examples of Particle-In-Cell Codes running on Nvidia GPU and Intel Phi architectures. This includes basic implementations in skeletons codes and full-scale development versions (encompassing 1D, 2D, and 3D codes) in Osiris. Both the similarities and differences between Intel's and Nvidia's hardware will be examined. Work supported by grants NSF ACI 1339893, DOE DE SC 000849, DOE DE SC 0008316, DOE DE NA 0001833, and DOE DE FC02 04ER 54780.

CSlib, a library to couple codes via Client/Server messaging

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

Plimpton, Steve

The CSlib is a small, portable library which enables two (or more) independent simulation codes to be coupled, by exchanging messages with each other. Both codes link to the library when they are built, and can them communicate with each other as they run. The messages contain data or instructions that the two codes send back-and-forth to each other. The messaging can take place via files, sockets, or MPI. The latter is a standard distributed-memory message-passing library.

Parser for Sabin-to-Mahoney Transition Model of Quasispecies Replication

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

Ecale Zhou, Carol

2016-01-03

This code is a data parse for preparing output from the Qspp agent-based stochastic simulation model for plotting in Excel. This code is specific to a set of simulations that were run for the purpose of preparing data for a publication. It is necessary to make this code open-source in order to publish the model code (Qspp), which has already been released. There is a necessity of assuring that results from using Qspp for a publication

Effects of virtualization on a scientific application - Running a hyperspectral radiative transfer code on virtual machines.

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

Tikotekar, Anand A; Vallee, Geoffroy R; Naughton III, Thomas J

2008-01-01

The topic of system-level virtualization has recently begun to receive interest for high performance computing (HPC). This is in part due to the isolation and encapsulation offered by the virtual machine. These traits enable applications to customize their environments and maintain consistent software configurations in their virtual domains. Additionally, there are mechanisms that can be used for fault tolerance like live virtual machine migration. Given these attractive benefits to virtualization, a fundamental question arises, how does this effect my scientific application? We use this as the premise for our paper and observe a real-world scientific code running on a Xenmore » virtual machine. We studied the effects of running a radiative transfer simulation, Hydrolight, on a virtual machine. We discuss our methodology and report observations regarding the usage of virtualization with this application.« less

Achieving behavioral control with millisecond resolution in a high-level programming environment

PubMed Central

Asaad, Wael F.; Eskandar, Emad N.

2008-01-01

The creation of psychophysical tasks for the behavioral neurosciences has generally relied upon low-level software running on a limited range of hardware. Despite the availability of software that allows the coding of behavioral tasks in high-level programming environments, many researchers are still reluctant to trust the temporal accuracy and resolution of programs running in such environments, especially when they run atop non-real-time operating systems. Thus, the creation of behavioral paradigms has been slowed by the intricacy of the coding required and their dissemination across labs has been hampered by the various types of hardware needed. However, we demonstrate here that, when proper measures are taken to handle the various sources of temporal error, accuracy can be achieved at the one millisecond time-scale that is relevant for the alignment of behavioral and neural events. PMID:18606188

Using individual differences to test the role of temporal and place cues in coding frequency modulation

PubMed Central

Whiteford, Kelly L.; Oxenham, Andrew J.

2015-01-01

The question of how frequency is coded in the peripheral auditory system remains unresolved. Previous research has suggested that slow rates of frequency modulation (FM) of a low carrier frequency may be coded via phase-locked temporal information in the auditory nerve, whereas FM at higher rates and/or high carrier frequencies may be coded via a rate-place (tonotopic) code. This hypothesis was tested in a cohort of 100 young normal-hearing listeners by comparing individual sensitivity to slow-rate (1-Hz) and fast-rate (20-Hz) FM at a carrier frequency of 500 Hz with independent measures of phase-locking (using dynamic interaural time difference, ITD, discrimination), level coding (using amplitude modulation, AM, detection), and frequency selectivity (using forward-masking patterns). All FM and AM thresholds were highly correlated with each other. However, no evidence was obtained for stronger correlations between measures thought to reflect phase-locking (e.g., slow-rate FM and ITD sensitivity), or between measures thought to reflect tonotopic coding (fast-rate FM and forward-masking patterns). The results suggest that either psychoacoustic performance in young normal-hearing listeners is not limited by peripheral coding, or that similar peripheral mechanisms limit both high- and low-rate FM coding. PMID:26627783

Using individual differences to test the role of temporal and place cues in coding frequency modulation.

PubMed

Whiteford, Kelly L; Oxenham, Andrew J

2015-11-01

The question of how frequency is coded in the peripheral auditory system remains unresolved. Previous research has suggested that slow rates of frequency modulation (FM) of a low carrier frequency may be coded via phase-locked temporal information in the auditory nerve, whereas FM at higher rates and/or high carrier frequencies may be coded via a rate-place (tonotopic) code. This hypothesis was tested in a cohort of 100 young normal-hearing listeners by comparing individual sensitivity to slow-rate (1-Hz) and fast-rate (20-Hz) FM at a carrier frequency of 500 Hz with independent measures of phase-locking (using dynamic interaural time difference, ITD, discrimination), level coding (using amplitude modulation, AM, detection), and frequency selectivity (using forward-masking patterns). All FM and AM thresholds were highly correlated with each other. However, no evidence was obtained for stronger correlations between measures thought to reflect phase-locking (e.g., slow-rate FM and ITD sensitivity), or between measures thought to reflect tonotopic coding (fast-rate FM and forward-masking patterns). The results suggest that either psychoacoustic performance in young normal-hearing listeners is not limited by peripheral coding, or that similar peripheral mechanisms limit both high- and low-rate FM coding.

Earth Global Reference Atmospheric Model (GRAM99): Short Course

NASA Technical Reports Server (NTRS)

Leslie, Fred W.; Justus, C. G.

2007-01-01

Earth-GRAM is a FORTRAN software package that can run on a variety of platforms including PC's. For any time and location in the Earth's atmosphere, Earth-GRAM provides values of atmospheric quantities such as temperature, pressure, density, winds, constituents, etc.. Dispersions (perturbations) of these parameters are also provided and have realistic correlations, means, and variances - useful for Monte Carlo analysis. Earth-GRAM is driven by observations including a tropospheric database available from the National Climatic Data Center. Although Earth-GRAM can be run in a "stand-alone" mode, many users incorporate it into their trajectory codes. The source code is distributed free-of-charge to eligible recipients.

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.

Spatial application of WEPS for estimating wind erosion in the Pacific Northwest

USDA-ARS?s Scientific Manuscript database

The Wind Erosion Prediction System (WEPS) is used to simulate soil erosion on croplands and was originally designed to run field scale simulations. This research is an extension of the WEPS model to run on multiple fields (grids) covering a larger region. We modified the WEPS source code to allow it...

Extending Orthogonal and Nearly Orthogonal Latin Hypercube Designs for Computer Simulation and Experimentation

DTIC Science & Technology

2006-12-01

The code was initially developed to be run within the netBeans IDE 5.04 running J2SE 5.0. During the course of the development, Eclipse SDK 3.2...covers the results from the research. Chapter V concludes and recommends future research. 4 netBeans

Man and Running. Russia's Best-Selling Book on Exercise, Health, and Medicine. A Worldwide Literature Search.

ERIC Educational Resources Information Center

Volkov, Vladimir M.; Milner, Evgeny G.

This book attempts to systematize and generalize the data of world literature concerning the advantages of fast walking and slow running for persons with various cardiovascular diseases. The information and the fitness program outlined are based on experience and research conducted at the Nadezha Health Club in Smolensk, Russia. Major risk factors…

PROTEUS-SN User Manual

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

Shemon, Emily R.; Smith, Micheal A.; Lee, Changho

2016-02-16

PROTEUS-SN is a three-dimensional, highly scalable, high-fidelity neutron transport code developed at Argonne National Laboratory. The code is applicable to all spectrum reactor transport calculations, particularly those in which a high degree of fidelity is needed either to represent spatial detail or to resolve solution gradients. PROTEUS-SN solves the second order formulation of the transport equation using the continuous Galerkin finite element method in space, the discrete ordinates approximation in angle, and the multigroup approximation in energy. PROTEUS-SN’s parallel methodology permits the efficient decomposition of the problem by both space and angle, permitting large problems to run efficiently on hundredsmore » of thousands of cores. PROTEUS-SN can also be used in serial or on smaller compute clusters (10’s to 100’s of cores) for smaller homogenized problems, although it is generally more computationally expensive than traditional homogenized methodology codes. PROTEUS-SN has been used to model partially homogenized systems, where regions of interest are represented explicitly and other regions are homogenized to reduce the problem size and required computational resources. PROTEUS-SN solves forward and adjoint eigenvalue problems and permits both neutron upscattering and downscattering. An adiabatic kinetics option has recently been included for performing simple time-dependent calculations in addition to standard steady state calculations. PROTEUS-SN handles void and reflective boundary conditions. Multigroup cross sections can be generated externally using the MC2-3 fast reactor multigroup cross section generation code or internally using the cross section application programming interface (API) which can treat the subgroup or resonance table libraries. PROTEUS-SN is written in Fortran 90 and also includes C preprocessor definitions. The code links against the PETSc, METIS, HDF5, and MPICH libraries. It optionally links against the MOAB library and is a part of the SHARP multi-physics suite for coupled multi-physics analysis of nuclear reactors. This user manual describes how to set up a neutron transport simulation with the PROTEUS-SN code. A companion methodology manual describes the theory and algorithms within PROTEUS-SN.« less

VizieR Online Data Catalog: Radiative forces for stellar envelopes (Seaton, 1997)

NASA Astrophysics Data System (ADS)

Seaton, M. J.; Yan, Y.; Mihalas, D.; Pradhan, A. K.

2000-02-01

(1) Primary data files, stages.zz These files give data for the calculation of radiative accelerations, GRAD, for elements with nuclear charge zz. Data are available for zz=06, 07, 08, 10, 11, 12, 13, 14, 16, 18, 20, 24, 25, 26 and 28. Calculations are made using data from the Opacity Project (see papers SYMP and IXZ). The data are given for each ionisation stage, j. They are tabulated on a mesh of (T, Ne, CHI) where T is temperature, Ne electron density and CHI is abundance multiplier. The files include data for ionisation fractions, for each (T, Ne). The file contents are described in the paper ACC and as comments in the code add.f (2) Code add.f This reads a file stages.zz and creates a file acc.zz giving radiative accelerations averaged over ionisation stages. The code prompts for names of input and output files. The code, as provided, gives equal weights (as defined in the paper ACC) to all stages. Th weights are set in SUBROUTINE WEIGHTS, which could be changed to give any weights preferred by the user. The dependence of diffusion coefficients on ionisation stage is given by a function ZET, which is defined in SUBROUTINE ZETA. The expressions used for ZET are as given in the paper. The user can change that subroutine if other expressions are preferred. The output file contains values, ZETBAR, of ZET, averaged over ionisation stages. (3) Files acc.zz Radiative accelerations computed using add.f as provided. The user will need to run the code add.f only if it is required to change the subroutines WEIGHTS or ZETA. The contents of the files acc.zz are described in the paper ACC and in comments contained in the code add.f. (4) Code accfit.f This code gives gives radiative accelerations, and some related data, for a stellar model. Methods used to interpolate data to the values of (T, RHO) for the stellar model are based on those used in the code opfit.for (see the paper OPF). The executable file accfit.com runs accfit.f. It uses a list of files given in accfit.files (see that file for further description). The mesh used for the abundance-multiplier CHI on the output file will generally be finer than that used in the input files acc.zz. The mesh to be used is specified on a file chi.dat. For a test run, the stellar model used is given in the file 10000_4.2 (Teff=10000 K, LOG10(g)=4.2) The output file from that test run is acc100004.2. The contents of the output file are described in the paper ACC and as comments in the code accfit.f. (5) The code diff.f This code reads the output file (e.g. acc1000004.2) created by accfit.f. For any specified depth point in the model and value of CHI, it gives values of radiative accelerations, the quantity ZETBAR required for calculation of diffusion coefficients, and Rosseland-mean opacities. The code prompts for input data. It creates a file recording all data calculated. The code diff.f is intended for incorporation, as a set of subroutines, in codes for diffusion calculations. (1 data file).

Flowfield computer graphics

NASA Technical Reports Server (NTRS)

Desautel, Richard

1993-01-01

The objectives of this research include supporting the Aerothermodynamics Branch's research by developing graphical visualization tools for both the branch's adaptive grid code and flow field ray tracing code. The completed research for the reporting period includes development of a graphical user interface (GUI) and its implementation into the NAS Flowfield Analysis Software Tool kit (FAST), for both the adaptive grid code (SAGE) and the flow field ray tracing code (CISS).

Annual Historical Report - AMEDD Activities, Calendar Year 1987

DTIC Science & Technology

1987-01-01

levels. Insulin levels were increased 2.2 fold with no change in glucagon. This profile is unlike that associated with weight loss due to fasting and may...were just as fast on the final PT test as the high mileage company. It appeared that for each mile run a quantifiable risk could be attached which was...various levels of fatness. Hum. Biol. 59:281-298, 1987. Knapik, J. J., B. H. Jones, C. Meredith, W. .J. Evans. Influence of 3.5 day fast on physical

Influence of a 3.5 Day Fast on Physical Performance Running Heading: Fasting and Performance,

DTIC Science & Technology

1986-01-01

induced atrophy. Two weeks of a hypocaloric diet has been shown to result in selective atrophy of Type II muscle fibers (28). However, it is unlike that...J, Marliss EB, Jeejeebhoy KN. Skeletal muse-le function during hypocaloric diets and fasting: a comparison with standard nutritional assessment...KN. Metabolic and structural changes in skeletal muscle during hypocaloric dieting . Am. J. Clin. Nutr. 1984; 39:503-513. 0 .4. .4.% Ii 20 29. Taylor H

Evaluation of Computational Codes for Underwater Hull Analysis Model Applications

DTIC Science & Technology

2014-02-05

desirable that the code can be run on a Windows operating system on the laptop, desktop, or workstation. The focus on Windows machines allows for...transition to such systems as operated on the Navy-Marine Corp Internet (NMCI). For each code the initial cost and yearly maintenance are identified...suggestions for reducing this burden to Department of Defense, Washington Headquarters Services, Directorate for Information Operations and Reports

The Fast Scattering Code (FSC): Validation Studies and Program Guidelines

NASA Technical Reports Server (NTRS)

Tinetti, Ana F.; Dunn, Mark H.

2011-01-01

The Fast Scattering Code (FSC) is a frequency domain noise prediction program developed at the NASA Langley Research Center (LaRC) to simulate the acoustic field produced by the interaction of known, time harmonic incident sound with bodies of arbitrary shape and surface impedance immersed in a potential flow. The code uses the equivalent source method (ESM) to solve an exterior 3-D Helmholtz boundary value problem (BVP) by expanding the scattered acoustic pressure field into a series of point sources distributed on a fictitious surface placed inside the actual scatterer. This work provides additional code validation studies and illustrates the range of code parameters that produce accurate results with minimal computational costs. Systematic noise prediction studies are presented in which monopole generated incident sound is scattered by simple geometric shapes - spheres (acoustically hard and soft surfaces), oblate spheroids, flat disk, and flat plates with various edge topologies. Comparisons between FSC simulations and analytical results and experimental data are presented.

An object-oriented, coprocessor-accelerated model for ice sheet simulations

NASA Astrophysics Data System (ADS)

Seddik, H.; Greve, R.

2013-12-01

Recently, numerous models capable of modeling the thermo-dynamics of ice sheets have been developed within the ice sheet modeling community. Their capabilities have been characterized by a wide range of features with different numerical methods (finite difference or finite element), different implementations of the ice flow mechanics (shallow-ice, higher-order, full Stokes) and different treatments for the basal and coastal areas (basal hydrology, basal sliding, ice shelves). Shallow-ice models (SICOPOLIS, IcIES, PISM, etc) have been widely used for modeling whole ice sheets (Greenland and Antarctica) due to the relatively low computational cost of the shallow-ice approximation but higher order (ISSM, AIF) and full Stokes (Elmer/Ice) models have been recently used to model the Greenland ice sheet. The advance in processor speed and the decrease in cost for accessing large amount of memory and storage have undoubtedly been the driving force in the commoditization of models with higher capabilities, and the popularity of Elmer/Ice (http://elmerice.elmerfem.com) with an active user base is a notable representation of this trend. Elmer/Ice is a full Stokes model built on top of the multi-physics package Elmer (http://www.csc.fi/english/pages/elmer) which provides the full machinery for the complex finite element procedure and is fully parallel (mesh partitioning with OpenMPI communication). Elmer is mainly written in Fortran 90 and targets essentially traditional processors as the code base was not initially written to run on modern coprocessors (yet adding support for the recently introduced x86 based coprocessors is possible). Furthermore, a truly modular and object-oriented implementation is required for quick adaptation to fast evolving capabilities in hardware (Fortran 2003 provides an object-oriented programming model while not being clean and requiring a tricky refactoring of Elmer code). In this work, the object-oriented, coprocessor-accelerated finite element code Sainou is introduced. Sainou is an Elmer fork which is reimplemented in Objective C and used for experimenting with ice sheet models running on coprocessors, essentially GPU devices. GPUs are highly parallel processors that provide opportunities for fine-grained parallelization of the full Stokes problem using the standard OpenCL language (http://www.khronos.org/opencl/) to access the device. Sainou is built upon a collection of Objective C base classes that service a modular kernel (itself a base class) which provides the core methods to solve the finite element problem. An early implementation of Sainou will be presented with emphasis on the object architecture and the strategies of parallelizations. The computation of a simple heat conduction problem is used to test the implementation which also provides experimental support for running the global matrix assembly on GPU.

Stability properties and fast ion confinement of hybrid tokamak plasma configurations

NASA Astrophysics Data System (ADS)

Graves, J. P.; Brunetti, D.; Pfefferle, D.; Faustin, J. M. P.; Cooper, W. A.; Kleiner, A.; Lanthaler, S.; Patten, H. W.; Raghunathan, M.

2015-11-01

In hybrid scenarios with flat q just above unity, extremely fast growing tearing modes are born from toroidal sidebands of the near resonant ideal internal kink mode. New scalings of the growth rate with the magnetic Reynolds number arise from two fluid effects and sheared toroidal flow. Non-linear saturated 1/1 dominant modes obtained from initial value stability calculation agree with the amplitude of the 1/1 component of a 3D VMEC equilibrium calculation. Viable and realistic equilibrium representation of such internal kink modes allow fast ion studies to be accurately established. Calculations of MAST neutral beam ion distributions using the VENUS-LEVIS code show very good agreement of observed impaired core fast ion confinement when long lived modes occur. The 3D ICRH code SCENIC also enables the establishment of minority RF distributions in hybrid plasmas susceptible to saturated near resonant internal kink modes.

A fast algorithm for identifying friends-of-friends halos

NASA Astrophysics Data System (ADS)

Feng, Y.; Modi, C.

2017-07-01

We describe a simple and fast algorithm for identifying friends-of-friends features and prove its correctness. The algorithm avoids unnecessary expensive neighbor queries, uses minimal memory overhead, and rejects slowdown in high over-density regions. We define our algorithm formally based on pair enumeration, a problem that has been heavily studied in fast 2-point correlation codes and our reference implementation employs a dual KD-tree correlation function code. We construct features in a hierarchical tree structure, and use a splay operation to reduce the average cost of identifying the root of a feature from O [ log L ] to O [ 1 ] (L is the size of a feature) without additional memory costs. This reduces the overall time complexity of merging trees from O [ L log L ] to O [ L ] , reducing the number of operations per splay by orders of magnitude. We next introduce a pruning operation that skips merge operations between two fully self-connected KD-tree nodes. This improves the robustness of the algorithm, reducing the number of merge operations in high density peaks from O [δ2 ] to O [ δ ] . We show that for cosmological data set the algorithm eliminates more than half of merge operations for typically used linking lengths b ∼ 0 . 2 (relative to mean separation). Furthermore, our algorithm is extremely simple and easy to implement on top of an existing pair enumeration code, reusing the optimization effort that has been invested in fast correlation function codes.

The fast decoding of Reed-Solomon codes using number theoretic transforms

NASA Technical Reports Server (NTRS)

Reed, I. S.; Welch, L. R.; Truong, T. K.

1976-01-01

It is shown that Reed-Solomon (RS) codes can be encoded and decoded by using a fast Fourier transform (FFT) algorithm over finite fields. The arithmetic utilized to perform these transforms requires only integer additions, circular shifts and a minimum number of integer multiplications. The computing time of this transform encoder-decoder for RS codes is less than the time of the standard method for RS codes. More generally, the field GF(q) is also considered, where q is a prime of the form K x 2 to the nth power + 1 and K and n are integers. GF(q) can be used to decode very long RS codes by an efficient FFT algorithm with an improvement in the number of symbols. It is shown that a radix-8 FFT algorithm over GF(q squared) can be utilized to encode and decode very long RS codes with a large number of symbols. For eight symbols in GF(q squared), this transform over GF(q squared) can be made simpler than any other known number theoretic transform with a similar capability. Of special interest is the decoding of a 16-tuple RS code with four errors.

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.

Concepts and Plans towards fast large scale Monte Carlo production for the ATLAS Experiment

NASA Astrophysics Data System (ADS)

Ritsch, E.; Atlas Collaboration

2014-06-01

The huge success of the physics program of the ATLAS experiment at the Large Hadron Collider (LHC) during Run 1 relies upon a great number of simulated Monte Carlo events. This Monte Carlo production takes the biggest part of the computing resources being in use by ATLAS as of now. In this document we describe the plans to overcome the computing resource limitations for large scale Monte Carlo production in the ATLAS Experiment for Run 2, and beyond. A number of fast detector simulation, digitization and reconstruction techniques are being discussed, based upon a new flexible detector simulation framework. To optimally benefit from these developments, a redesigned ATLAS MC production chain is presented at the end of this document.

Warthog: Coupling Status Update

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

Hart, Shane W. D.; Reardon, Bradley T.

The Warthog code was developed to couple codes that are developed in both the Multi-Physics Object-Oriented Simulation Environment (MOOSE) from Idaho National Laboratory (INL) and SHARP from Argonne National Laboratory (ANL). The initial phase of this work, focused on coupling the neutronics code PROTEUS with the fuel performance code BISON. The main technical challenge involves mapping the power density solution determined by PROTEUS to the fuel in BISON. This presents a challenge since PROTEUS uses the MOAB mesh format, but BISON, like all other MOOSE codes, uses the libMesh format. When coupling the different codes, one must consider that Warthogmore » is a light-weight MOOSE-based program that uses the Data Transfer Kit (DTK) to transfer data between the various mesh types. Users set up inputs for the codes they want to run, and then Warthog transfers the data between them. Currently Warthog supports XSProc from SCALE or the Sub-Group Application Programming Interface (SGAPI) in PROTEUS for generating cross sections. It supports arbitrary geometries using PROTEUS and BISON. DTK will transfer power densities and temperatures between the codes where the domains overlap. In the past fiscal year (FY), much work has gone into demonstrating two-way coupling for simple pin cells of various materials. XSProc was used to calculate the cross sections, which were then passed to PROTEUS in an external file. PROTEUS calculates the fission/power density, and Warthog uses DTK to pass this information to BISON, where it is used as the heat source. BISON then calculates the temperature profile of the pin cell and sends it back to XSProc to obtain the temperature corrected cross sections. This process is repeated until the convergence criteria (tolerance on BISON solve, or number of time steps) is reached. Models have been constructed and run for both uranium oxide and uranium silicide fuels. These models demonstrate a clear difference in power shape that is not accounted for in a stand-alone BISON run. Future work involves improving the user interface (UI), likely through integration with the Nuclear Energy Advanced Modeling and Simulation (NEAMS) Workbench. Furthermore, automating the input creation would ease the user experience. The next priority is to continue coupling the work with other codes in the SHARP package. Efforts on other projects include work to couple the Nek5000 thermo-hydraulics code to MOOSE, but this is in the preliminary stages.« less

LTCP 2D Graphical User Interface. Application Description and User's Guide

NASA Technical Reports Server (NTRS)

Ball, Robert; Navaz, Homayun K.

1996-01-01

A graphical user interface (GUI) written for NASA's LTCP (Liquid Thrust Chamber Performance) 2 dimensional computational fluid dynamic code is described. The GUI is written in C++ for a desktop personal computer running under a Microsoft Windows operating environment. Through the use of common and familiar dialog boxes, features, and tools, the user can easily and quickly create and modify input files for the LTCP code. In addition, old input files used with the LTCP code can be opened and modified using the GUI. The application is written in C++ for a desktop personal computer running under a Microsoft Windows operating environment. The program and its capabilities are presented, followed by a detailed description of each menu selection and the method of creating an input file for LTCP. A cross reference is included to help experienced users quickly find the variables which commonly need changes. Finally, the system requirements and installation instructions are provided.

GASPRNG: GPU accelerated scalable parallel random number generator library

NASA Astrophysics Data System (ADS)

Gao, Shuang; Peterson, Gregory D.

2013-04-01

Graphics processors represent a promising technology for accelerating computational science applications. Many computational science applications require fast and scalable random number generation with good statistical properties, so they use the Scalable Parallel Random Number Generators library (SPRNG). We present the GPU Accelerated SPRNG library (GASPRNG) to accelerate SPRNG in GPU-based high performance computing systems. GASPRNG includes code for a host CPU and CUDA code for execution on NVIDIA graphics processing units (GPUs) along with a programming interface to support various usage models for pseudorandom numbers and computational science applications executing on the CPU, GPU, or both. This paper describes the implementation approach used to produce high performance and also describes how to use the programming interface. The programming interface allows a user to be able to use GASPRNG the same way as SPRNG on traditional serial or parallel computers as well as to develop tightly coupled programs executing primarily on the GPU. We also describe how to install GASPRNG and use it. To help illustrate linking with GASPRNG, various demonstration codes are included for the different usage models. GASPRNG on a single GPU shows up to 280x speedup over SPRNG on a single CPU core and is able to scale for larger systems in the same manner as SPRNG. Because GASPRNG generates identical streams of pseudorandom numbers as SPRNG, users can be confident about the quality of GASPRNG for scalable computational science applications. Catalogue identifier: AEOI_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEOI_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: UTK license. No. of lines in distributed program, including test data, etc.: 167900 No. of bytes in distributed program, including test data, etc.: 1422058 Distribution format: tar.gz Programming language: C and CUDA. Computer: Any PC or workstation with NVIDIA GPU (Tested on Fermi GTX480, Tesla C1060, Tesla M2070). Operating system: Linux with CUDA version 4.0 or later. Should also run on MacOS, Windows, or UNIX. Has the code been vectorized or parallelized?: Yes. Parallelized using MPI directives. RAM: 512 MB˜ 732 MB (main memory on host CPU, depending on the data type of random numbers.) / 512 MB (GPU global memory) Classification: 4.13, 6.5. Nature of problem: Many computational science applications are able to consume large numbers of random numbers. For example, Monte Carlo simulations are able to consume limitless random numbers for the computation as long as resources for the computing are supported. Moreover, parallel computational science applications require independent streams of random numbers to attain statistically significant results. The SPRNG library provides this capability, but at a significant computational cost. The GASPRNG library presented here accelerates the generators of independent streams of random numbers using graphical processing units (GPUs). Solution method: Multiple copies of random number generators in GPUs allow a computational science application to consume large numbers of random numbers from independent, parallel streams. GASPRNG is a random number generators library to allow a computational science application to employ multiple copies of random number generators to boost performance. Users can interface GASPRNG with software code executing on microprocessors and/or GPUs. Running time: The tests provided take a few minutes to run.

EBR-II Static Neutronic Calculations by PHISICS / MCNP6 codes

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

Paolo Balestra; Carlo Parisi; Andrea Alfonsi

2016-02-01

The International Atomic Energy Agency (IAEA) launched a Coordinated Research Project (CRP) on the Shutdown Heat Removal Tests (SHRT) performed in the '80s at the Experimental fast Breeder Reactor EBR-II, USA. The scope of the CRP is to improve and validate the simulation tools for the study and the design of the liquid metal cooled fast reactors. Moreover, training of the next generation of fast reactor analysts is being also considered the other scope of the CRP. In this framework, a static neutronic model was developed, using state-of-the art neutron transport codes like SCALE/PHISICS (deterministic solution) and MCNP6 (stochastic solution).more » Comparison between both solutions is briefly illustrated in this summary.« less

Fast particles identification in programmable form at level-0 trigger by means of the 3D-Flow system

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

Crosetto, Dario B.

1998-10-30

The 3D-Flow Processor system is a new, technology-independent concept in very fast, real-time system architectures. Based on either an FPGA or an ASIC implementation, it can address, in a fully programmable manner, applications where commercially available processors would fail because of throughput requirements. Possible applications include filtering-algorithms (pattern recognition) from the input of multiple sensors, as well as moving any input validated by these filtering-algorithms to a single output channel. Both operations can easily be implemented on a 3D-Flow system to achieve a real-time processing system with a very short lag time. This system can be built either with off-the-shelfmore » FPGAs or, for higher data rates, with CMOS chips containing 4 to 16 processors each. The basic building block of the system, a 3D-Flow processor, has been successfully designed in VHDL code written in ''Generic HDL'' (mostly made of reusable blocks that are synthesizable in different technologies, or FPGAs), to produce a netlist for a four-processor ASIC featuring 0.35 micron CBA (Ceil Base Array) technology at 3.3 Volts, 884 mW power dissipation at 60 MHz and 63.75 mm sq. die size. The same VHDL code has been targeted to three FPGA manufacturers (Altera EPF10K250A, ORCA-Lucent Technologies 0R3T165 and Xilinx XCV1000). A complete set of software tools, the 3D-Flow System Manager, equally applicable to ASIC or FPGA implementations, has been produced to provide full system simulation, application development, real-time monitoring, and run-time fault recovery. Today's technology can accommodate 16 processors per chip in a medium size die, at a cost per processor of less than $5 based on the current silicon die/size technology cost.« less

MATH77 - A LIBRARY OF MATHEMATICAL SUBPROGRAMS FOR FORTRAN 77, RELEASE 4.0

NASA Technical Reports Server (NTRS)

Lawson, C. L.

1994-01-01

MATH77 is a high quality library of ANSI FORTRAN 77 subprograms implementing contemporary algorithms for the basic computational processes of science and engineering. The portability of MATH77 meets the needs of present-day scientists and engineers who typically use a variety of computing environments. Release 4.0 of MATH77 contains 454 user-callable and 136 lower-level subprograms. Usage of the user-callable subprograms is described in 69 sections of the 416 page users' manual. The topics covered by MATH77 are indicated by the following list of chapter titles in the users' manual: Mathematical Functions, Pseudo-random Number Generation, Linear Systems of Equations and Linear Least Squares, Matrix Eigenvalues and Eigenvectors, Matrix Vector Utilities, Nonlinear Equation Solving, Curve Fitting, Table Look-Up and Interpolation, Definite Integrals (Quadrature), Ordinary Differential Equations, Minimization, Polynomial Rootfinding, Finite Fourier Transforms, Special Arithmetic , Sorting, Library Utilities, Character-based Graphics, and Statistics. Besides subprograms that are adaptations of public domain software, MATH77 contains a number of unique packages developed by the authors of MATH77. Instances of the latter type include (1) adaptive quadrature, allowing for exceptional generality in multidimensional cases, (2) the ordinary differential equations solver used in spacecraft trajectory computation for JPL missions, (3) univariate and multivariate table look-up and interpolation, allowing for "ragged" tables, and providing error estimates, and (4) univariate and multivariate derivative-propagation arithmetic. MATH77 release 4.0 is a subroutine library which has been carefully designed to be usable on any computer system that supports the full ANSI standard FORTRAN 77 language. It has been successfully implemented on a CRAY Y/MP computer running UNICOS, a UNISYS 1100 computer running EXEC 8, a DEC VAX series computer running VMS, a Sun4 series computer running SunOS, a Hewlett-Packard 720 computer running HP-UX, a Macintosh computer running MacOS, and an IBM PC compatible computer running MS-DOS. Accompanying the library is a set of 196 "demo" drivers that exercise all of the user-callable subprograms. The FORTRAN source code for MATH77 comprises 109K lines of code in 375 files with a total size of 4.5Mb. The demo drivers comprise 11K lines of code and 418K. Forty-four percent of the lines of the library code and 29% of those in the demo code are comment lines. The standard distribution medium for MATH77 is a .25 inch streaming magnetic tape cartridge in UNIX tar format. It is also available on a 9track 1600 BPI magnetic tape in VAX BACKUP format and a TK50 tape cartridge in VAX BACKUP format. An electronic copy of the documentation is included on the distribution media. Previous releases of MATH77 have been used over a number of years in a variety of JPL applications. MATH77 Release 4.0 was completed in 1992. MATH77 is a copyrighted work with all copyright vested in NASA.

JCL (Job Control Language) Procedures to Run the Hull Code on the Cyber 205 Computer Installed on CSIRONET.

DTIC Science & Technology

1986-11-01

START THE RUN>>> USERNUIDNUPW. CHARGEGROUPNPID. SETJOB, DC= NO . COMMENT . GET CR ATTACH THE INPUT DATA TO GO TO VSOS. GET, INDATA=DATFILE/NA. IFE...NtPW. CHARGEGROUPNPID. SETTL, 200. SETJOB. DC= NO . COMMENT . RUN SAIL ON NOS TO GENERATE THE MAIN PROGRAM. PURGE, SAl LOUT/NA. PURGE, PROG-PROBLEMID...NOSPASS. CHARGEDFCDFCPR.F. SETJOB. DC= NO . COMMENT . GET OR ATTACH THE INPUT DATA To Go To VSOS. GET. INDATA=MYDATA/NA. IFE. .NOT.FILE(INDATA.AS) .DOATT

Searching for Fast Radio Bursts with the Advanced Laser Interferometer Gravitational-wave Observatory (LIGO)

NASA Astrophysics Data System (ADS)

Fisher, Ryan Patrick; Hughey, Brennan; Howell, Eric; LIGO Collaboration

2018-01-01

Although Fast Radio Bursts (FRB) are being detected with increasing frequency, their progenitor systems are still mostly a mystery. We present the plan to conduct targeted searches for gravitational-wave counterparts to these FRB events in the data from the first and second observing runs of the Advanced Laser Interferometer Gravitational-wave Observatory (LIGO).

Evaluation of the Ross fast solution of Richards’ equation in unfavourable conditions for standard finite element methods

NASA Astrophysics Data System (ADS)

Crevoisier, David; Chanzy, André; Voltz, Marc

2009-06-01

Ross [Ross PJ. Modeling soil water and solute transport - fast, simplified numerical solutions. Agron J 2003;95:1352-61] developed a fast, simplified method for solving Richards' equation. This non-iterative 1D approach, using Brooks and Corey [Brooks RH, Corey AT. Hydraulic properties of porous media. Hydrol. papers, Colorado St. Univ., Fort Collins; 1964] hydraulic functions, allows a significant reduction in computing time while maintaining the accuracy of the results. The first aim of this work is to confirm these results in a more extensive set of problems, including those that would lead to serious numerical difficulties for the standard numerical method. The second aim is to validate a generalisation of the Ross method to other mathematical representations of hydraulic functions. The Ross method is compared with the standard finite element model, Hydrus-1D [Simunek J, Sejna M, Van Genuchten MTh. The HYDRUS-1D and HYDRUS-2D codes for estimating unsaturated soil hydraulic and solutes transport parameters. Agron Abstr 357; 1999]. Computing time, accuracy of results and robustness of numerical schemes are monitored in 1D simulations involving different types of homogeneous soils, grids and hydrological conditions. The Ross method associated with modified Van Genuchten hydraulic functions [Vogel T, Cislerova M. On the reliability of unsaturated hydraulic conductivity calculated from the moisture retention curve. Transport Porous Media 1988;3:1-15] proves in every tested scenario to be more robust numerically, and the compromise of computing time/accuracy is seen to be particularly improved on coarse grids. Ross method run from 1.25 to 14 times faster than Hydrus-1D.

Acute Caffeinated Coffee Consumption Does not Improve Time Trial Performance in an 800-m Run: A Randomized, Double-Blind, Crossover, Placebo-Controlled Study.

PubMed

Marques, Alexandre C; Jesus, Alison A; Giglio, Bruna M; Marini, Ana C; Lobo, Patrícia C B; Mota, João F; Pimentel, Gustavo D

2018-05-23

Studies evaluating caffeinated coffee (CAF) can reveal ergogenic effects; however, studies on the effects of caffeinated coffee on running are scarce and controversial. To investigate the effects of CAF consumption compared to decaffeinated coffee (DEC) consumption on time trial performances in an 800-m run in overnight-fasting runners. A randomly counterbalanced, double-blind, crossover, placebo-controlled study was conducted with 12 healthy adult males with experience in amateur endurance running. Participants conducted two trials on two different occasions, one day with either CAF or DEC, with a one-week washout. After arriving at the data collection site, participants consumed the soluble CAF (5.5 mg/kg of caffeine) or DEC and after 60 min the run was started. Before and after the 800-m race, blood pressure and lactate and glucose concentrations were measured. At the end of the run, the ratings of perceived exertion (RPE) scale was applied. The runners were light consumers of habitual caffeine, with an average ingestion of 91.3 mg (range 6⁻420 mg/day). Time trial performances did not change between trials (DEF: 2.38 + 0.10 vs. CAF: 2.39 + 0.09 min, p = 0.336), nor did the RPE (DEC: 16.5 + 2.68 vs. CAF: 17.0 + 2.66, p = 0.326). No difference between the trials was observed for glucose and lactate concentrations, or for systolic and diastolic blood pressure levels. CAF consumption failed to enhance the time trial performance of an 800-m run in overnight-fasting runners, when compared with DEC ingestion. In addition, no change was found in RPE, blood pressure levels, or blood glucose and lactate concentrations between the two trials.

Combustor Simulation

NASA Technical Reports Server (NTRS)

Norris, Andrew

2003-01-01

The goal was to perform 3D simulation of GE90 combustor, as part of full turbofan engine simulation. Requirements of high fidelity as well as fast turn-around time require massively parallel code. National Combustion Code (NCC) was chosen for this task as supports up to 999 processors and includes state-of-the-art combustion models. Also required is ability to take inlet conditions from compressor code and give exit conditions to turbine code.

Force field development with GOMC, a fast new Monte Carlo molecular simulation code

NASA Astrophysics Data System (ADS)

Mick, Jason Richard

In this work GOMC (GPU Optimized Monte Carlo) a new fast, flexible, and free molecular Monte Carlo code for the simulation atomistic chemical systems is presented. The results of a large Lennard-Jonesium simulation in the Gibbs ensemble is presented. Force fields developed using the code are also presented. To fit the models a quantitative fitting process is outlined using a scoring function and heat maps. The presented n-6 force fields include force fields for noble gases and branched alkanes. These force fields are shown to be the most accurate LJ or n-6 force fields to date for these compounds, capable of reproducing pure fluid behavior and binary mixture behavior to a high degree of accuracy.

Identifying subassemblies by ultrasound to prevent fuel handling error in sodium fast reactors: First test performed in water

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

Paumel, Kevin; Lhuillier, Christian

2015-07-01

Identifying subassemblies by ultrasound is a method that is being considered to prevent handling errors in sodium fast reactors. It is based on the reading of a code (aligned notches) engraved on the subassembly head by an emitting/receiving ultrasonic sensor. This reading is carried out in sodium with high temperature transducers. The resulting one-dimensional C-scan can be likened to a binary code expressing the subassembly type and number. The first test performed in water investigated two parameters: width and depth of the notches. The code remained legible for notches as thin as 1.6 mm wide. The impact of the depthmore » seems minor in the range under investigation. (authors)« less

Running Records and First Grade English Learners: An Analysis of Language Related Errors

ERIC Educational Resources Information Center

Briceño, Allison; Klein, Adria F.

2018-01-01

The purpose of this study was to determine if first-grade English Learners made patterns of language related errors when reading, and if so, to identify those patterns and how teachers coded language related errors when analyzing English Learners' running records. Using research from the fields of both literacy and Second Language Acquisition, we…

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

Thorson, L.D.

A description is given of a new version of the TRUMP (UCRL-14754) computer code, NOTRUMP, which runs on both the CDC-7600 and CRAY-1. There are slight differences in the input and major changes in output capability. A postprocessor, AFTER, is available to manipulate some of the new output features. Old data decks for TRUMP will normally run with only minor changes.

Evolution of perceived footwear comfort over a prolonged running session.

PubMed

Hintzy, F; Cavagna, J; Horvais, N

2015-12-01

The purpose of this study was to investigate the subjective perception of overall footwear comfort over a prolonged running session. Ten runners performed two similar sessions consisting of a 13-km trail run (5 laps of 2.6 km) as fast as possible. The overall footwear comfort was evaluated before running and at the end of each lap with a 150-mm visual analogic scale, as well as speed, heart rate and rate of perceived exertion. The results showed that both overall footwear comfort and speed decreased consistently during the run session, and significantly after 44 min of running (i.e. the 3rd lap). It could be hypothesized that the deterioration of overall footwear comfort was explained by mechanical and energetical parameter changes with time and/or fatigue occurring at the whole body, foot and footwear levels. These results justify the use of a prolonged running test for running footwear comfort evaluation. Copyright © 2015 Elsevier Ltd. All rights reserved.

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

Mao, Shoudi; He, Jiansen; Yang, Liping

The impact of an overtaking fast shock on a magnetic cloud (MC) is a pivotal process in CME–CME (CME: coronal mass ejection) interactions and CME–SIR (SIR: stream interaction region) interactions. MC with a strong and rotating magnetic field is usually deemed a crucial part of CMEs. To study the impact of a fast shock on an MC, we perform a 2.5 dimensional numerical magnetohydrodynamic simulation. Two cases are run in this study: without and with impact by fast shock. In the former case, the MC expands gradually from its initial state and drives a relatively slow magnetic reconnection with themore » ambient magnetic field. Analyses of forces near the core of the MC as a whole body indicates that the solar gravity is quite small compared to the Lorentz force and the pressure gradient force. In the second run, a fast shock propagates, relative to the background plasma, at a speed twice that of the perpendicular fast magnetosonic speed, catches up with and takes over the MC. Due to the penetration of the fast shock, the MC is highly compressed and heated, with the temperature growth rate enhanced by a factor of about 10 and the velocity increased to about half of the shock speed. The magnetic reconnection with ambient magnetic field is also sped up by a factor of two to four in reconnection rate as a result of the enhanced density of the current sheet, which is squeezed by the forward motion of the shocked MC.« less

Decay heat of sodium fast reactor: Comparison of experimental measurements on the PHENIX reactor with calculations performed with the French DARWIN package

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

Benoit, J. C.; Bourdot, P.; Eschbach, R.

2012-07-01

A Decay Heat (DH) experiment on the whole core of the French Sodium-Cooled Fast Reactor PHENIX has been conducted in May 2008. The measurements began an hour and a half after the shutdown of the reactor and lasted twelve days. It is one of the experiments used for the experimental validation of the depletion code DARWIN thereby confirming the excellent performance of the aforementioned code. Discrepancies between measured and calculated decay heat do not exceed 8%. (authors)

Reproducibility and Transparency in Ocean-Climate Modeling

NASA Astrophysics Data System (ADS)

Hannah, N.; Adcroft, A.; Hallberg, R.; Griffies, S. M.

2015-12-01

Reproducibility is a cornerstone of the scientific method. Within geophysical modeling and simulation achieving reproducibility can be difficult, especially given the complexity of numerical codes, enormous and disparate data sets, and variety of supercomputing technology. We have made progress on this problem in the context of a large project - the development of new ocean and sea ice models, MOM6 and SIS2. Here we present useful techniques and experience.We use version control not only for code but the entire experiment working directory, including configuration (run-time parameters, component versions), input data and checksums on experiment output. This allows us to document when the solutions to experiments change, whether due to code updates or changes in input data. To avoid distributing large input datasets we provide the tools for generating these from the sources, rather than provide raw input data.Bugs can be a source of non-determinism and hence irreproducibility, e.g. reading from or branching on uninitialized memory. To expose these we routinely run system tests, using a memory debugger, multiple compilers and different machines. Additional confidence in the code comes from specialised tests, for example automated dimensional analysis and domain transformations. This has entailed adopting a code style where we deliberately restrict what a compiler can do when re-arranging mathematical expressions.In the spirit of open science, all development is in the public domain. This leads to a positive feedback, where increased transparency and reproducibility makes using the model easier for external collaborators, who in turn provide valuable contributions. To facilitate users installing and running the model we provide (version controlled) digital notebooks that illustrate and record analysis of output. This has the dual role of providing a gross, platform-independent, testing capability and a means to documents model output and analysis.

Using Intel Xeon Phi to accelerate the WRF TEMF planetary boundary layer scheme

NASA Astrophysics Data System (ADS)

Mielikainen, Jarno; Huang, Bormin; Huang, Allen

2014-05-01

The Weather Research and Forecasting (WRF) model is designed for numerical weather prediction and atmospheric research. The WRF software infrastructure consists of several components such as dynamic solvers and physics schemes. Numerical models are used to resolve the large-scale flow. However, subgrid-scale parameterizations are for an estimation of small-scale properties (e.g., boundary layer turbulence and convection, clouds, radiation). Those have a significant influence on the resolved scale due to the complex nonlinear nature of the atmosphere. For the cloudy planetary boundary layer (PBL), it is fundamental to parameterize vertical turbulent fluxes and subgrid-scale condensation in a realistic manner. A parameterization based on the Total Energy - Mass Flux (TEMF) that unifies turbulence and moist convection components produces a better result that the other PBL schemes. For that reason, the TEMF scheme is chosen as the PBL scheme we optimized for Intel Many Integrated Core (MIC), which 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 optimization results for TEMF planetary boundary layer scheme. The optimizations that were performed were quite generic in nature. Those optimizations included vectorization of the code to utilize vector units inside each CPU. Furthermore, memory access was improved by scalarizing some of the intermediate arrays. The results show that the optimization improved MIC performance by 14.8x. Furthermore, the optimizations increased CPU performance by 2.6x compared to the original multi-threaded code on quad core Intel Xeon E5-2603 running at 1.8 GHz. Compared to the optimized code running on a single CPU socket the optimized MIC code is 6.2x faster.

Cooperative solutions coupling a geometry engine and adaptive solver codes

NASA Technical Reports Server (NTRS)

Dickens, Thomas P.

1995-01-01

Follow-on work has progressed in using Aero Grid and Paneling System (AGPS), a geometry and visualization system, as a dynamic real time geometry monitor, manipulator, and interrogator for other codes. In particular, AGPS has been successfully coupled with adaptive flow solvers which iterate, refining the grid in areas of interest, and continuing on to a solution. With the coupling to the geometry engine, the new grids represent the actual geometry much more accurately since they are derived directly from the geometry and do not use refits to the first-cut grids. Additional work has been done with design runs where the geometric shape is modified to achieve a desired result. Various constraints are used to point the solution in a reasonable direction which also more closely satisfies the desired results. Concepts and techniques are presented, as well as examples of sample case studies. Issues such as distributed operation of the cooperative codes versus running all codes locally and pre-calculation for performance are discussed. Future directions are considered which will build on these techniques in light of changing computer environments.

A generic archive protocol and an implementation

NASA Technical Reports Server (NTRS)

Jordan, J. M.; Jennings, D. G.; Mcglynn, T. A.; Ruggiero, N. G.; Serlemitsos, T. A.

1992-01-01

Archiving vast amounts of data has become a major part of every scientific space mission today. The Generic Archive/Retrieval Services Protocol (GRASP) addresses the question of how to archive the data collected in an environment where the underlying hardware archives may be rapidly changing. GRASP is a device independent specification defining a set of functions for storing and retrieving data from an archive, as well as other support functions. GRASP is divided into two levels: the Transfer Interface and the Action Interface. The Transfer Interface is computer/archive independent code while the Action Interface contains code which is dedicated to each archive/computer addressed. Implementations of the GRASP specification are currently available for DECstations running Ultrix, Sparcstations running SunOS, and microVAX/VAXstation 3100's. The underlying archive is assumed to function as a standard Unix or VMS file system. The code, written in C, is a single suite of files. Preprocessing commands define the machine unique code sections in the device interface. The implementation was written, to the greatest extent possible, using only ANSI standard C functions.

PVM Wrapper

NASA Technical Reports Server (NTRS)

Katz, Daniel

2004-01-01

PVM Wrapper is a software library that makes it possible for code that utilizes the Parallel Virtual Machine (PVM) software library to run using the message-passing interface (MPI) software library, without needing to rewrite the entire code. PVM and MPI are the two most common software libraries used for applications that involve passing of messages among parallel computers. Since about 1996, MPI has been the de facto standard. Codes written when PVM was popular often feature patterns of {"initsend," "pack," "send"} and {"receive," "unpack"} calls. In many cases, these calls are not contiguous and one set of calls may even exist over multiple subroutines. These characteristics make it difficult to obtain equivalent functionality via a single MPI "send" call. Because PVM Wrapper is written to run with MPI- 1.2, some PVM functions are not permitted and must be replaced - a task that requires some programming expertise. The "pvm_spawn" and "pvm_parent" function calls are not replaced, but a programmer can use "mpirun" and knowledge of the ranks of parent and child tasks with supplied macroinstructions to enable execution of codes that use "pvm_spawn" and "pvm_parent."

No positive influence of ingesting chia seed oil on human running performance.

PubMed

Nieman, David C; Gillitt, Nicholas D; Meaney, Mary Pat; Dew, Dustin A

2015-05-15

Runners (n = 24) reported to the laboratory in an overnight fasted state at 8:00 am on two occasions separated by at least two weeks. After providing a blood sample at 8:00 am, subjects ingested 0.5 liters flavored water alone or 0.5 liters water with 7 kcal kg-1 chia seed oil (random order), provided another blood sample at 8:30 am, and then started running to exhaustion (~70% VO2max). Additional blood samples were collected immediately post- and 1-h post-exercise. Despite elevations in plasma alpha-linolenic acid (ALA) during the chia seed oil (337%) versus water trial (35%) (70.8 ± 8.6, 20.3 ± 1.8 μg mL(-1), respectively, p < 0.001), run time to exhaustion did not differ between trials (1.86 ± 0.10, 1.91 ± 0.13 h, p = 0.577, respectively). No trial differences were found for respiratory exchange ratio (RER) (0.92 ± 0.01), oxygen consumption, ventilation, ratings of perceived exertion (RPE), and plasma glucose and blood lactate. Significant post-run increases were measured for total leukocyte counts, plasma cortisol, and plasma cytokines (Interleukin-6 (IL-6), Interleukin-8 (IL-8), Interleukin-10 (IL-10), and Tumor necrosis factors-α (TNF-α)), with no trial differences. Chia seed oil supplementation compared to water alone in overnight fasted runners before and during prolonged, intensive running caused an elevation in plasma ALA, but did not enhance run time to exhaustion, alter RER, or counter elevations in cortisol and inflammatory outcome measures.

Posttest calculation of the PBF LOC-11B and LOC-11C experiments using RELAP4/MOD6. [PWR

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

Hendrix, C.E.

Comparisons between RELAP4/MOD6, Update 4 code-calculated and measured experimental data are presented for the PBF LOC-11C and LOC-11B experiments. Independent code verification techniques are now being developed and this study represents a preliminary effort applying structured criteria for developing computer models, selecting code input, and performing base-run analyses. Where deficiencies are indicated in the base-case representation of the experiment, methods of code and criteria improvement are developed and appropriate recommendations are made.

Photoionization and High Density Gas

NASA Technical Reports Server (NTRS)

Kallman, T.; Bautista, M.; White, Nicholas E. (Technical Monitor)

2002-01-01

We present results of calculations using the XSTAR version 2 computer code. This code is loosely based on the XSTAR v.1 code which has been available for public use for some time. However it represents an improvement and update in several major respects, including atomic data, code structure, user interface, and improved physical description of ionization/excitation. In particular, it now is applicable to high density situations in which significant excited atomic level populations are likely to occur. We describe the computational techniques and assumptions, and present sample runs with particular emphasis on high density situations.

Multitasking for flows about multiple body configurations using the chimera grid scheme

NASA Technical Reports Server (NTRS)

Dougherty, F. C.; Morgan, R. L.

1987-01-01

The multitasking of a finite-difference scheme using multiple overset meshes is described. In this chimera, or multiple overset mesh approach, a multiple body configuration is mapped using a major grid about the main component of the configuration, with minor overset meshes used to map each additional component. This type of code is well suited to multitasking. Both steady and unsteady two dimensional computations are run on parallel processors on a CRAY-X/MP 48, usually with one mesh per processor. Flow field results are compared with single processor results to demonstrate the feasibility of running multiple mesh codes on parallel processors and to show the increase in efficiency.

Comprehensive approach to fast ion measurements in the beam-driven FRC

NASA Astrophysics Data System (ADS)

Magee, Richard; Smirnov, Artem; Onofri, Marco; Dettrick, Sean; Korepanov, Sergey; Knapp, Kurt; the TAE Team

2015-11-01

The C-2U experiment combines tangential neutral beam injection, edge biasing, and advanced recycling control to explore the sustainment of field-reversed configuration (FRC) plasmas. To study fast ion confinement in such advanced, beam-driven FRCs, a synergetic technique was developed that relies on the measurements of the DD fusion reaction products and the hybrid code Q2D, which treats the plasma as a fluid and the fast ions kinetically. Data from calibrated neutron and proton detectors are used in a complementary fashion to constrain the simulations: neutron detectors measure the volume integrated fusion rate to constrain the total number of fast ions, while proton detectors with multiple lines of sight through the plasma constrain the axial profile of fast ions. One application of this technique is the diagnosis of fast ion energy transfer and pitch angle scattering. A parametric numerical study was conducted, in which additional ad hoc loss and scattering terms of varying strengths were introduced in the code and constrained with measurement. Initial results indicate that the energy transfer is predominantly classical, while, in some cases, non-classical pitch angle scattering can be observed.

An introduction to QR Codes: linking libraries and mobile patrons.

PubMed

Hoy, Matthew B

2011-01-01

QR codes, or "Quick Response" codes, are two-dimensional barcodes that can be scanned by mobile smartphone cameras. These codes can be used to provide fast access to URLs, telephone numbers, and short passages of text. With the rapid adoption of smartphones, librarians are able to use QR codes to promote services and help library users find materials quickly and independently. This article will explain what QR codes are, discuss how they can be used in the library, and describe issues surrounding their use. A list of resources for generating and scanning QR codes is also provided.

ORBIT modelling of fast particle redistribution induced by sawtooth instability

NASA Astrophysics Data System (ADS)

Kim, Doohyun; Podestà, Mario; Poli, Francesca; Princeton Plasma Physics Laboratory Team

2017-10-01

Initial tests on NSTX-U show that introducing energy selectivity for sawtooth (ST) induced fast ion redistribution improves the agreement between experimental and simulated quantities, e.g. neutron rate. Thus, it is expected that a proper description of the fast particle redistribution due to ST can improve the modelling of ST instability and interpretation of experiments using a transport code. In this work, we use ORBIT code to characterise the redistribution of fast particles. In order to simulate a ST crash, a spatial and temporal displacement is implemented as ξ (ρ , t , θ , ϕ) = ∑ξmn (ρ , t) cos (mθ + nϕ) to produce perturbed magnetic fields from the equilibrium field B-> , δB-> = ∇ × (ξ-> × B->) , which affect the fast particle distribution. From ORBIT simulations, we find suitable amplitudes of ξ for each ST crash to reproduce the experimental results. The comparison of the simulation and the experimental results will be discussed as well as the dependence of fast ion redistribution on fast ion phase space variables (i.e. energy, magnetic moment and toroidal angular momentum). Work supported by the U.S. Department of Energy, Office of Science, Office of Fusion Energy Sciences under Contract Number DE-AC02-09CH11466.

The MOLDY short-range molecular dynamics package

NASA Astrophysics Data System (ADS)

Ackland, G. J.; D'Mellow, K.; Daraszewicz, S. L.; Hepburn, D. J.; Uhrin, M.; Stratford, K.

2011-12-01

We describe a parallelised version of the MOLDY molecular dynamics program. This Fortran code is aimed at systems which may be described by short-range potentials and specifically those which may be addressed with the embedded atom method. This includes a wide range of transition metals and alloys. MOLDY provides a range of options in terms of the molecular dynamics ensemble used and the boundary conditions which may be applied. A number of standard potentials are provided, and the modular structure of the code allows new potentials to be added easily. The code is parallelised using OpenMP and can therefore be run on shared memory systems, including modern multicore processors. Particular attention is paid to the updates required in the main force loop, where synchronisation is often required in OpenMP implementations of molecular dynamics. We examine the performance of the parallel code in detail and give some examples of applications to realistic problems, including the dynamic compression of copper and carbon migration in an iron-carbon alloy. Program summaryProgram title: MOLDY Catalogue identifier: AEJU_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJU_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 2 No. of lines in distributed program, including test data, etc.: 382 881 No. of bytes in distributed program, including test data, etc.: 6 705 242 Distribution format: tar.gz Programming language: Fortran 95/OpenMP Computer: Any Operating system: Any Has the code been vectorised or parallelized?: Yes. OpenMP is required for parallel execution RAM: 100 MB or more Classification: 7.7 Nature of problem: Moldy addresses the problem of many atoms (of order 10 6) interacting via a classical interatomic potential on a timescale of microseconds. It is designed for problems where statistics must be gathered over a number of equivalent runs, such as measuring thermodynamic properities, diffusion, radiation damage, fracture, twinning deformation, nucleation and growth of phase transitions, sputtering etc. In the vast majority of materials, the interactions are non-pairwise, and the code must be able to deal with many-body forces. Solution method: Molecular dynamics involves integrating Newton's equations of motion. MOLDY uses verlet (for good energy conservation) or predictor-corrector (for accurate trajectories) algorithms. It is parallelised using open MP. It also includes a static minimisation routine to find the lowest energy structure. Boundary conditions for surfaces, clusters, grain boundaries, thermostat (Nose), barostat (Parrinello-Rahman), and externally applied strain are provided. The initial configuration can be either a repeated unit cell or have all atoms given explictly. Initial velocities are generated internally, but it is also possible to specify the velocity of a particular atom. A wide range of interatomic force models are implemented, including embedded atom, Morse or Lennard-Jones. Thus the program is especially well suited to calculations of metals. Restrictions: The code is designed for short-ranged potentials, and there is no Ewald sum. Thus for long range interactions where all particles interact with all others, the order- N scaling will fail. Different interatomic potential forms require recompilation of the code. Additional comments: There is a set of associated open-source analysis software for postprocessing and visualisation. This includes local crystal structure recognition and identification of topological defects. Running time: A set of test modules for running time are provided. The code scales as order N. The parallelisation shows near-linear scaling with number of processors in a shared memory environment. A typical run of a few tens of nanometers for a few nanoseconds will run on a timescale of days on a multiprocessor desktop.

Recovery of coded wire tags at a caspian tern colony in San Francisco Bay: A technique to evaluate impacts of avian predation on juvenile salmonids

USGS Publications Warehouse

Evans, A.F.; Roby, D.D.; Collis, K.; Cramer, B.M.; Sheggeby, J.A.; Adrean, L.J.; Battaglia, D.S.; Lyons, Donald E.

2011-01-01

We recovered coded wire tags (CWTs) from a colony of Caspian terns Hydroprogne caspia on Brooks Island in San Francisco Bay, California, to evaluate predation on juvenile salmonids originating from the Sacramento and San Joaquin rivers. Subsamples of colony substrate representing 11.7% of the nesting habitat used by the terns yielded 2,079 salmonid CWTs from fish released and subsequently consumed by terns in 2008. The estimated number of CWTs deposited on the entire tern colony was 40,143 (ranging from 26,763 to 80,288), once adjustments were made to account for tag loss and the total amount of nesting habitat used by terns. Tags ingested by terns and then egested on the colony were undamaged, and the tags' complete numeric codes were still identifiable. The CWTs found on the tern colony indicated that hatchery Chinook salmon Oncorhynchus tshawytscha trucked to and released in San Pablo Bay were significantly more likely to be consumed by Caspian terns than Chinook salmon that migrated in-river to the bay; 99.7% of all tags recovered were from bay-released Chinook salmon. Of the CWTs recovered on the tern colony, 98.0% were from fall-run Chinook salmon, indicating a higher susceptibility to tern predation than for the spring run type. None of the approximately 518,000 wild Chinook salmon that were coded-wire-tagged and released in the basin were recovered on the tern colony, suggesting that the impacts on wild, U.S. Endangered Species Act-listed Chinook salmon populations were minimal in 2008. Overall, we estimate that 0.3% of the approximately 12.3 million coded-wire-tagged Chinook salmon released in the basin in 2008 were subsequently consumed by Caspian terns from the Brooks Island colony. These results indicate that CWTs implanted in juvenile salmon can be recovered from a piscivorous waterbird colony and used to evaluate smolt losses for runs that are tagged. Abstract We recovered coded wire tags (CWTs) from a colony of Caspian terns Hydroprogne caspia on Brooks Island in San Francisco Bay, California, to evaluate predation on juvenile salmonids originating from the Sacramento and San Joaquin rivers. Subsamples of colony substrate representing 11.7% of the nesting habitat used by the terns yielded 2,079 salmonid CWTs from fish released and subsequently consumed by terns in 2008. The estimated number of CWTs deposited on the entire tern colony was 40,143 (ranging from 26,763 to 80,288), once adjustments were made to account for tag loss and the total amount of nesting habitat used by terns. Tags ingested by terns and then egested on the colony were undamaged, and the tags' complete numeric codes were still identifiable. The CWTs found on the tern colony indicated that hatchery Chinook salmon Oncorhynchus tshawytscha trucked to and released in San Pablo Bay were significantly more likely to be consumed by Caspian terns than Chinook salmon that migrated in-river to the bay; 99.7% of all tags recovered were from bay-released Chinook salmon. Of the CWTs recovered on the tern colony, 98.0% were from fall-run Chinook salmon, indicating a higher susceptibility to tern predation than for the spring run type. None of the approximately 518,000 wild Chinook salmon that were coded-wire-tagged and released in the basin were recovered on the tern colony, suggesting that the impacts on wild, U.S. Endangered Species Act-listed Chinook salmon populations were minimal in 2008. Overall, we estimate that 0.3% of the approximately 12.3 million coded-wire-tagged Chinook salmon released in the basin in 2008 were subsequently consumed by Caspian terns from the Brooks Island colony. These results indicate that CWTs implanted in juvenile salmon can be recovered from a piscivorous waterbird colony and used to evaluate smolt losses for runs that are tagged ?? American Fisheries Society 2011.

Running-related injuries in school-age children and adolescents treated in emergency departments from 1994 through 2007.

PubMed

Mehl, Ann J; Nelson, Nicolas G; McKenzie, Lara B

2011-02-01

Running for exercise is a popular way to motivate children to be physically active. Running-related injuries are well studied in adults but little information exists for children and adolescents. Through use of the National Electronic Injury Surveillance System database, cases of running-related injuries were selected by using activity codes for exercise (which included running and jogging). Sample weights were used to calculate national estimates. An estimated 225 344 children and adolescents 6 to 18 years old were treated in US emergency departments for running-related injuries. The annual number of cases increased by 34.0% over the study period. One third of the injuries involved a running-related fall and more than one half of the injuries occurred at school. The majority of injuries occurred to the lower extremities and resulted in a sprain or strain. These findings emphasize the need for scientific evidence-based guidelines for pediatric running. The high proportion of running-related falls warrants further research.

Study of the effect of sawteeth on fast ions and neutron emission in MAST using a neutron camera

NASA Astrophysics Data System (ADS)

Cecconello, M.; Sperduti, A.; the MAST team

2018-05-01

The effect of the sawtooth instability on the confinement of fast ions on MAST, and the impact it has on the neutron emission, has been studied in detail using the TRANSP/NUBEAM codes coupled to a full orbit following code. The sawtooth models in TRANSP/NUBEAM indicate that, on MAST, passing and trapped fast ions are redistributed in approximately equal number and on a level that is consistent with the observations. It has not been possible to discriminate between the different sawtooth models since their predictions are all compatible with the neutron camera observations. Full orbit calculations of the fast ion motion have been used to estimate the characteristic time scales and energy thresholds that according to theoretical predictions govern the fast ions redistribution: no energy threshold for the redistribution for either passing and trapped fast ions was found. The characteristic times have, however, frequencies that are comparable with the frequencies of a m = 1, n = 1 perturbation and its harmonics with toroidal mode numbers n=2, \\ldots , 4, suggesting that on spherical tokamaks, in addition to the classical sawtooth-induced transport mechanisms of fast ions by attachment to the evolving perturbation and the associated E × B drift, a resonance mechanism between the m = 1 perturbation and the fast ions orbits might be at play.

Automatic analysis (aa): efficient neuroimaging workflows and parallel processing using Matlab and XML.

PubMed

Cusack, Rhodri; Vicente-Grabovetsky, Alejandro; Mitchell, Daniel J; Wild, Conor J; Auer, Tibor; Linke, Annika C; Peelle, Jonathan E

2014-01-01

Recent years have seen neuroimaging data sets becoming richer, with larger cohorts of participants, a greater variety of acquisition techniques, and increasingly complex analyses. These advances have made data analysis pipelines complicated to set up and run (increasing the risk of human error) and time consuming to execute (restricting what analyses are attempted). Here we present an open-source framework, automatic analysis (aa), to address these concerns. Human efficiency is increased by making code modular and reusable, and managing its execution with a processing engine that tracks what has been completed and what needs to be (re)done. Analysis is accelerated by optional parallel processing of independent tasks on cluster or cloud computing resources. A pipeline comprises a series of modules that each perform a specific task. The processing engine keeps track of the data, calculating a map of upstream and downstream dependencies for each module. Existing modules are available for many analysis tasks, such as SPM-based fMRI preprocessing, individual and group level statistics, voxel-based morphometry, tractography, and multi-voxel pattern analyses (MVPA). However, aa also allows for full customization, and encourages efficient management of code: new modules may be written with only a small code overhead. aa has been used by more than 50 researchers in hundreds of neuroimaging studies comprising thousands of subjects. It has been found to be robust, fast, and efficient, for simple-single subject studies up to multimodal pipelines on hundreds of subjects. It is attractive to both novice and experienced users. aa can reduce the amount of time neuroimaging laboratories spend performing analyses and reduce errors, expanding the range of scientific questions it is practical to address.

Prevalence of Food and Beverage Brands in Movies: 1996–2005

PubMed Central

Sutherland, Lisa A.; MacKenzie, Todd; Purvis, Lisa A.; Dalton, Madeline

2010-01-01

OBJECTIVE The objective of this study was to describe food and beverage brand placements in a large representative sample of popular movies. METHODS We identified and coded brand placements for foods, beverages, and food retail establishments in the top 20 US box office movie hits for each year from 1996 to 2005. We also coded general movie characteristics (Motion Picture Association of America rating, run time, genre, and information about major characters). We summarized the number and types of food, beverage, and food retail establishment brands by movie characteristics and also identified manufacturers that are associated with each of the brands. RESULTS Of the 200 movies coded, 138 (69%) contained at least 1 food, beverage, or food retail establishment brand. Movies rated PG-13 and R were significantly more likely to have brand placements compared with movies in other rating categories. Comedies, action/adventures, and horror films had more brand placements than other genres. We did not detect a significant difference in the number of movies with brand placements or mean number of placements per movie by year of movie release. A total of 1180 brand placements were identified and verified, including 427 food, 425 beverage, and 328 food retail establishment brand placements. Candy/confections (26%) and salty snacks (21%) were the most prevalent food brands, sugar-sweetened beverages (76%) were the most prevalent beverage brands, and fast food composed two thirds of the food retail establishment brand placements. CONCLUSIONS Food, beverage, and food retail establishment brands are frequently portrayed in movies, and most of the brand placements are for energy-dense, nutrient-poor foods or product lines. Movies are a potent source of advertising to children, which has been largely overlooked. PMID:20142289

GenomeVista

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

Poliakov, Alexander; Couronne, Olivier

2002-11-04

Aligning large vertebrate genomes that are structurally complex poses a variety of problems not encountered on smaller scales. Such genomes are rich in repetitive elements and contain multiple segmental duplications, which increases the difficulty of identifying true orthologous SNA segments in alignments. The sizes of the sequences make many alignment algorithms designed for comparing single proteins extremely inefficient when processing large genomic intervals. We integrated both local and global alignment tools and developed a suite of programs for automatically aligning large vertebrate genomes and identifying conserved non-coding regions in the alignments. Our method uses the BLAT local alignment program tomore » find anchors on the base genome to identify regions of possible homology for a query sequence. These regions are postprocessed to find the best candidates which are then globally aligned using the AVID global alignment program. In the last step conserved non-coding segments are identified using VISTA. Our methods are fast and the resulting alignments exhibit a high degree of sensitivity, covering more than 90% of known coding exons in the human genome. The GenomeVISTA software is a suite of Perl programs that is built on a MySQL database platform. The scheduler gets control data from the database, builds a queve of jobs, and dispatches them to a PC cluster for execution. The main program, running on each node of the cluster, processes individual sequences. A Perl library acts as an interface between the database and the above programs. The use of a separate library allows the programs to function independently of the database schema. The library also improves on the standard Perl MySQL database interfere package by providing auto-reconnect functionality and improved error handling.« less

Prevalence of food and beverage brands in movies: 1996-2005.

PubMed

Sutherland, Lisa A; Mackenzie, Todd; Purvis, Lisa A; Dalton, Madeline

2010-03-01

The objective of this study was to describe food and beverage brand placements in a large representative sample of popular movies. We identified and coded brand placements for foods, beverages, and food retail establishments in the top 20 US box office movie hits for each year from 1996 to 2005. We also coded general movie characteristics (Motion Picture Association of America rating, run time, genre, and information about major characters). We summarized the number and types of food, beverage, and food retail establishment brands by movie characteristics and also identified manufacturers that are associated with each of the brands. Of the 200 movies coded, 138 (69%) contained at least 1 food, beverage, or food retail establishment brand. Movies rated PG-13 and R were significantly more likely to have brand placements compared with movies in other rating categories. Comedies, action/adventures, and horror films had more brand placements than other genres. We did not detect a significant difference in the number of movies with brand placements or mean number of placements per movie by year of movie release. A total of 1180 brand placements were identified and verified, including 427 food, 425 beverage, and 328 food retail establishment brand placements. Candy/confections (26%) and salty snacks (21%) were the most prevalent food brands, sugar-sweetened beverages (76%) were the most prevalent beverage brands, and fast food composed two thirds of the food retail establishment brand placements. Food, beverage, and food retail establishment brands are frequently portrayed in movies, and most of the brand placements are for energy-dense, nutrient-poor foods or product lines. Movies are a potent source of advertising to children, which has been largely overlooked.

Onboard Image Processing System for Hyperspectral Sensor

PubMed Central

Hihara, Hiroki; Moritani, Kotaro; Inoue, Masao; Hoshi, Yoshihiro; Iwasaki, Akira; Takada, Jun; Inada, Hitomi; Suzuki, Makoto; Seki, Taeko; Ichikawa, Satoshi; Tanii, Jun

2015-01-01

Onboard image processing systems for a hyperspectral sensor have been developed in order to maximize image data transmission efficiency for large volume and high speed data downlink capacity. Since more than 100 channels are required for hyperspectral sensors on Earth observation satellites, fast and small-footprint lossless image compression capability is essential for reducing the size and weight of a sensor system. A fast lossless image compression algorithm has been developed, and is implemented in the onboard correction circuitry of sensitivity and linearity of Complementary Metal Oxide Semiconductor (CMOS) sensors in order to maximize the compression ratio. The employed image compression method is based on Fast, Efficient, Lossless Image compression System (FELICS), which is a hierarchical predictive coding method with resolution scaling. To improve FELICS’s performance of image decorrelation and entropy coding, we apply a two-dimensional interpolation prediction and adaptive Golomb-Rice coding. It supports progressive decompression using resolution scaling while still maintaining superior performance measured as speed and complexity. Coding efficiency and compression speed enlarge the effective capacity of signal transmission channels, which lead to reducing onboard hardware by multiplexing sensor signals into a reduced number of compression circuits. The circuitry is embedded into the data formatter of the sensor system without adding size, weight, power consumption, and fabrication cost. PMID:26404281

Fast All-Sky Radiation Model for Solar Applications (FARMS): A Brief Overview of Mechanisms, Performance, and Applications: Preprint

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

Xie, Yu; Sengupta, Manajit

Solar radiation can be computed using radiative transfer models, such as the Rapid Radiation Transfer Model (RRTM) and its general circulation model applications, and used for various energy applications. Due to the complexity of computing radiation fields in aerosol and cloudy atmospheres, simulating solar radiation can be extremely time-consuming, but many approximations--e.g., the two-stream approach and the delta-M truncation scheme--can be utilized. To provide a new fast option for computing solar radiation, we developed the Fast All-sky Radiation Model for Solar applications (FARMS) by parameterizing the simulated diffuse horizontal irradiance and direct normal irradiance for cloudy conditions from the RRTMmore » runs using a 16-stream discrete ordinates radiative transfer method. The solar irradiance at the surface was simulated by combining the cloud irradiance parameterizations with a fast clear-sky model, REST2. To understand the accuracy and efficiency of the newly developed fast model, we analyzed FARMS runs using cloud optical and microphysical properties retrieved using GOES data from 2009-2012. The global horizontal irradiance for cloudy conditions was simulated using FARMS and RRTM for global circulation modeling with a two-stream approximation and compared to measurements taken from the U.S. Department of Energy's Atmospheric Radiation Measurement Climate Research Facility Southern Great Plains site. Our results indicate that the accuracy of FARMS is comparable to or better than the two-stream approach; however, FARMS is approximately 400 times more efficient because it does not explicitly solve the radiative transfer equation for each individual cloud condition. Radiative transfer model runs are computationally expensive, but this model is promising for broad applications in solar resource assessment and forecasting. It is currently being used in the National Solar Radiation Database, which is publicly available from the National Renewable Energy Laboratory at http://nsrdb.nrel.gov.« less

Development of 1D Particle-in-Cell Code and Simulation of Plasma-Wall Interactions

NASA Astrophysics Data System (ADS)

Rose, Laura P.

This thesis discusses the development of a 1D particle-in-cell (PIC) code and the analysis of plasma-wall interactions. The 1D code (Plasma and Wall Simulation -- PAWS) is a kinetic simulation of plasma done by treating both electrons and ions as particles. The goal of this thesis is to study near wall plasma interaction to better understand the mechanism that occurs in this region. The main focus of this investigation is the effects that secondary electrons have on the sheath profile. The 1D code is modeled using the PIC method. Treating both the electrons and ions as macroparticles the field is solved on each node and weighted to each macro particle. A pre-ionized plasma was loaded into the domain and the velocities of particles were sampled from the Maxwellian distribution. An important part of this code is the boundary conditions at the wall. If a particle hits the wall a secondary electron may be produced based on the incident energy. To study the sheath profile the simulations were run for various cases. Varying background neutral gas densities were run with the 2D code and compared to experimental values. Different wall materials were simulated to show their effects of SEE. In addition different SEE yields were run, including one study with very high SEE yields to show the presence of a space charge limited sheath. Wall roughness was also studied with the 1D code using random angles of incidence. In addition to the 1D code, an external 2D code was also used to investigate wall roughness without secondary electrons. The roughness profiles where created upon investigation of wall roughness inside Hall Thrusters based off of studies done on lifetime erosion of the inner and outer walls of these devices. The 2D code, Starfish[33], is a general 2D axisymmetric/Cartesian code for modeling a wide a range of plasma and rarefied gas problems. These results show that higher SEE yield produces a smaller sheath profile and that wall roughness produces a lower SEE yield. Modeling near wall interactions is not a simple or perfected task. Due to the lack of a second dimension and a sputtering model it is not possible with this study to show the positive effects wall roughness could have on Hall thruster performance since roughness occurs from the negative affect of sputtering.

Prototype part task trainer: A remote manipulator system simulator

NASA Technical Reports Server (NTRS)

Shores, David

1989-01-01

The Part Task Trainer program (PTT) is a kinematic simulation of the Remote Manipulator System (RMS) for the orbiter. The purpose of the PTT is to supply a low cost man-in-the-loop simulator, allowing the student to learn operational procedures which then can be used in the more expensive full scale simulators. PTT will allow the crew members to work on their arm operation skills without the need for other people running the simulation. The controlling algorithms for the arm were coded out of the Functional Subsystem Requirements Document to ensure realistic operation of the simulation. Relying on the hardware of the workstation to provide fast refresh rates for full shaded images allows the simulation to be run on small low cost stand alone work stations, removing the need to be tied into a multi-million dollar computer for the simulation. PTT will allow the student to make errors which in full scale mock up simulators might cause failures or damage hardware. On the screen the user is shown a graphical representation of the RMS control panel in the aft cockpit of the orbiter, along with a main view window and up to six trunion and guide windows. The dials drawn on the panel may be turned to select the desired mode of operation. The inputs controlling the arm are read from a chair with a Translational Hand Controller (THC) and a Rotational Hand Controller (RHC) attached to it.

Consequence analysis in LPG installation using an integrated computer package.

PubMed

Ditali, S; Colombi, M; Moreschini, G; Senni, S

2000-01-07

This paper presents the prototype of the computer code, Atlantide, developed to assess the consequences associated with accidental events that can occur in a LPG storage plant. The characteristic of Atlantide is to be simple enough but at the same time adequate to cope with consequence analysis as required by Italian legislation in fulfilling the Seveso Directive. The application of Atlantide is appropriate for LPG storage/transferring installations. The models and correlations implemented in the code are relevant to flashing liquid releases, heavy gas dispersion and other typical phenomena such as BLEVE/Fireball. The computer code allows, on the basis of the operating/design characteristics, the study of the relevant accidental events from the evaluation of the release rate (liquid, gaseous and two-phase) in the unit involved, to the analysis of the subsequent evaporation and dispersion, up to the assessment of the final phenomena of fire and explosion. This is done taking as reference simplified Event Trees which describe the evolution of accidental scenarios, taking into account the most likely meteorological conditions, the different release situations and other features typical of a LPG installation. The limited input data required and the automatic linking between the single models, that are activated in a defined sequence, depending on the accidental event selected, minimize both the time required for the risk analysis and the possibility of errors. Models and equations implemented in Atlantide have been selected from public literature or in-house developed software and tailored with the aim to be easy to use and fast to run but, nevertheless, able to provide realistic simulation of the accidental event as well as reliable results, in terms of physical effects and hazardous areas. The results have been compared with those of other internationally recognized codes and with the criteria adopted by Italian authorities to verify the Safety Reports for LPG installations. A brief of the theoretical basis of each model implemented in Atlantide and an example of application are included in the paper.

nIFTY galaxy cluster simulations - III. The similarity and diversity of galaxies and subhaloes

NASA Astrophysics Data System (ADS)

Elahi, Pascal J.; Knebe, Alexander; Pearce, Frazer R.; Power, Chris; Yepes, Gustavo; Cui, Weiguang; Cunnama, Daniel; Kay, Scott T.; Sembolini, Federico; Beck, Alexander M.; Davé, Romeel; February, Sean; Huang, Shuiyao; Katz, Neal; McCarthy, Ian G.; Murante, Giuseppe; Perret, Valentin; Puchwein, Ewald; Saro, Alexandro; Teyssier, Romain

2016-05-01

We examine subhaloes and galaxies residing in a simulated Λ cold dark matter galaxy cluster (M^crit_{200}=1.1× 10^{15} h^{-1} M_{⊙}) produced by hydrodynamical codes ranging from classic smooth particle hydrodynamics (SPH), newer SPH codes, adaptive and moving mesh codes. These codes use subgrid models to capture galaxy formation physics. We compare how well these codes reproduce the same subhaloes/galaxies in gravity-only, non-radiative hydrodynamics and full feedback physics runs by looking at the overall subhalo/galaxy distribution and on an individual object basis. We find that the subhalo population is reproduced to within ≲10 per cent for both dark matter only and non-radiative runs, with individual objects showing code-to-code scatter of ≲0.1 dex, although the gas in non-radiative simulations shows significant scatter. Including feedback physics significantly increases the diversity. Subhalo mass and Vmax distributions vary by ≈20 per cent. The galaxy populations also show striking code-to-code variations. Although the Tully-Fisher relation is similar in almost all codes, the number of galaxies with 109 h- 1 M⊙ ≲ M* ≲ 1012 h- 1 M⊙ can differ by a factor of 4. Individual galaxies show code-to-code scatter of ˜0.5 dex in stellar mass. Moreover, systematic differences exist, with some codes producing galaxies 70 per cent smaller than others. The diversity partially arises from the inclusion/absence of active galactic nucleus feedback. Our results combined with our companion papers demonstrate that subgrid physics is not just subject to fine-tuning, but the complexity of building galaxies in all environments remains a challenge. We argue that even basic galaxy properties, such as stellar mass to halo mass, should be treated with errors bars of ˜0.2-0.4 dex.

Use of statecharts in the modelling of dynamic behaviour in the ATLAS DAQ prototype-1

NASA Astrophysics Data System (ADS)

Croll, P.; Duval, P.-Y.; Jones, R.; Kolos, S.; Sari, R. F.; Wheeler, S.

1998-08-01

Many applications within the ATLAS DAQ prototype-1 system have complicated dynamic behaviour which can be successfully modelled in terms of states and transitions between states. Previously, state diagrams implemented as finite-state machines have been used. Although effective, they become ungainly as system size increases. Harel statecharts address this problem by implementing additional features such as hierarchy and concurrency. The CHSM object-oriented language system is freeware which implements Harel statecharts as concurrent, hierarchical, finite-state machines (CHSMs). An evaluation of this language system by the ATLAS DAQ group has shown it to be suitable for describing the dynamic behaviour of typical DAQ applications. The language is currently being used to model the dynamic behaviour of the prototype-1 run-control system. The design is specified by means of a CHSM description file, and C++ code is obtained by running the CHSM compiler on the file. In parallel with the modelling work, a code generator has been developed which translates statecharts, drawn using the StP CASE tool, into the CHSM language. C++ code, describing the dynamic behaviour of the run-control system, has been successfully generated directly from StP statecharts using the CHSM generator and compiler. The validity of the design was tested using the simulation features of the Statemate CASE tool.

Testing hydrodynamics schemes in galaxy disc simulations

NASA Astrophysics Data System (ADS)

Few, C. G.; Dobbs, C.; Pettitt, A.; Konstandin, L.

2016-08-01

We examine how three fundamentally different numerical hydrodynamics codes follow the evolution of an isothermal galactic disc with an external spiral potential. We compare an adaptive mesh refinement code (RAMSES), a smoothed particle hydrodynamics code (SPHNG), and a volume-discretized mesh-less code (GIZMO). Using standard refinement criteria, we find that RAMSES produces a disc that is less vertically concentrated and does not reach such high densities as the SPHNG or GIZMO runs. The gas surface density in the spiral arms increases at a lower rate for the RAMSES simulations compared to the other codes. There is also a greater degree of substructure in the SPHNG and GIZMO runs and secondary spiral arms are more pronounced. By resolving the Jeans length with a greater number of grid cells, we achieve more similar results to the Lagrangian codes used in this study. Other alterations to the refinement scheme (adding extra levels of refinement and refining based on local density gradients) are less successful in reducing the disparity between RAMSES and SPHNG/GIZMO. Although more similar, SPHNG displays different density distributions and vertical mass profiles to all modes of GIZMO (including the smoothed particle hydrodynamics version). This suggests differences also arise which are not intrinsic to the particular method but rather due to its implementation. The discrepancies between codes (in particular, the densities reached in the spiral arms) could potentially result in differences in the locations and time-scales for gravitational collapse, and therefore impact star formation activity in more complex galaxy disc simulations.

Application of the RNS3D Code to a Circular-Rectangular Transition Duct With and Without Inlet Swirl and Comparison with Experiments

NASA Technical Reports Server (NTRS)

Cavicchi, Richard H.

1999-01-01

Circular-rectangular transition ducts are used between engine exhausts and nozzles with rectangular cross sections that are designed for high performance aircraft. NASA Glenn Research Center has made experimental investigations of a series of circular-rectangular transition ducts to provide benchmark flow data for comparison with numerical calculations. These ducts are all designed with superellipse cross sections to facilitate grid generation. In response to this challenge, the three-dimensional RNS3D code has been applied to one of these transition ducts. This particular duct has a length-to-inlet diameter ratio of 1.5 and an exit-plane aspect ratio of 3.0. The inlet Mach number is 0.35. Two GRC experiments and the code were run for this duct without inlet swirl. One GRC experiment and the code were also run with inlet swirl. With no inlet swirl the code was successful in predicting pressures and secondary flow conditions, including a pair of counter-rotating vortices at both sidewalls of the exit plane. All these phenomena have been reported from the two GRC experiments. However, these vortices were suppressed in the one experiment when inlet swirl was used; whereas the RNS3D code still predicted them. The experiment was unable to provide data near the sidewalls, the very region where the vortices were predicted.

How to review 4 million lines of ATLAS code

NASA Astrophysics Data System (ADS)

Stewart, Graeme A.; Lampl, Walter; ATLAS Collaboration

2017-10-01

As the ATLAS Experiment prepares to move to a multi-threaded framework (AthenaMT) for Run3, we are faced with the problem of how to migrate 4 million lines of C++ source code. This code has been written over the past 15 years and has often been adapted, re-written or extended to the changing requirements and circumstances of LHC data taking. The code was developed by different authors, many of whom are no longer active, and under the deep assumption that processing ATLAS data would be done in a serial fashion. In order to understand the scale of the problem faced by the ATLAS software community, and to plan appropriately the significant efforts posed by the new AthenaMT framework, ATLAS embarked on a wide ranging review of our offline code, covering all areas of activity: event generation, simulation, trigger, reconstruction. We discuss the difficulties in even logistically organising such reviews in an already busy community, how to examine areas in sufficient depth to learn key areas in need of upgrade, yet also to finish the reviews in a timely fashion. We show how the reviews were organised and how the ouptuts were captured in a way that the sub-system communities could then tackle the problems uncovered on a realistic timeline. Further, we discuss how the review has inuenced the overall planning for the Run 3 ATLAS offline code.

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.

Velocity, safety, or both? How do balance and strength of goal conflicts affect drivers' behaviour, feelings and physiological responses?

PubMed

Schmidt-Daffy, Martin; Brandenburg, Stefan; Beliavski, Alina

2013-06-01

Motivational models of driving behaviour agree that choice of speed is modulated by drivers' goals. Whilst it is accepted that some goals favour fast driving and others favour safe driving, little is known about the interplay of these conflicting goals. In the present study, two aspects of this interplay are investigated: the balance of conflict and the strength of conflict. Thirty-two participants completed several simulated driving runs in which fast driving was rewarded with a monetary gain if the end of the track was reached. However, unpredictably, some runs ended with the appearance of a deer. In these runs, fast driving was punished with a monetary loss. The ratio between the magnitudes of gains and losses varied in order to manipulate the balance of conflict. The absolute magnitudes of both gains and losses altered the strength of conflict. Participants drove slower, reported an increase in anxiety-related feelings, and showed indications of physiological arousal if there was more money at stake. In contrast, only marginal effects of varying the ratio between gains and losses were observed. Results confirm that the strength of a safety-velocity conflict is an important determinant of drivers' behaviour, feelings, and physiological responses. The lack of evidence for the balance of conflict playing a role suggests that in each condition, participants subjectively weighted the loss higher than the gain (loss aversion). It is concluded that the interplay of the subjective values that drivers attribute to objective incentives for fast and safe driving is a promising field for future research. Incorporating this knowledge into motivational theories of driving behaviour might improve their contribution to the design of adequate road safety measures. Copyright © 2013 Elsevier Ltd. All rights reserved.

The NYU inverse swept wing code

NASA Technical Reports Server (NTRS)

Bauer, F.; Garabedian, P.; Mcfadden, G.

1983-01-01

An inverse swept wing code is described that is based on the widely used transonic flow program FLO22. The new code incorporates a free boundary algorithm permitting the pressure distribution to be prescribed over a portion of the wing surface. A special routine is included to calculate the wave drag, which can be minimized in its dependence on the pressure distribution. An alternate formulation of the boundary condition at infinity was introduced to enhance the speed and accuracy of the code. A FORTRAN listing of the code and a listing of a sample run are presented. There is also a user's manual as well as glossaries of input and output parameters.

Status report on the 'Merging' of the Electron-Cloud Code POSINST with the 3-D Accelerator PIC CODE WARP

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

Vay, J.-L.; Furman, M.A.; Azevedo, A.W.

2004-04-19

We have integrated the electron-cloud code POSINST [1] with WARP [2]--a 3-D parallel Particle-In-Cell accelerator code developed for Heavy Ion Inertial Fusion--so that the two can interoperate. Both codes are run in the same process, communicate through a Python interpreter (already used in WARP), and share certain key arrays (so far, particle positions and velocities). Currently, POSINST provides primary and secondary sources of electrons, beam bunch kicks, a particle mover, and diagnostics. WARP provides the field solvers and diagnostics. Secondary emission routines are provided by the Tech-X package CMEE.

SU-E-T-493: Accelerated Monte Carlo Methods for Photon Dosimetry Using a Dual-GPU System and CUDA.

PubMed

Liu, T; Ding, A; Xu, X

2012-06-01

To develop a Graphics Processing Unit (GPU) based Monte Carlo (MC) code that accelerates dose calculations on a dual-GPU system. We simulated a clinical case of prostate cancer treatment. A voxelized abdomen phantom derived from 120 CT slices was used containing 218×126×60 voxels, and a GE LightSpeed 16-MDCT scanner was modeled. A CPU version of the MC code was first developed in C++ and tested on Intel Xeon X5660 2.8GHz CPU, then it was translated into GPU version using CUDA C 4.1 and run on a dual Tesla m 2 090 GPU system. The code was featured with automatic assignment of simulation task to multiple GPUs, as well as accurate calculation of energy- and material- dependent cross-sections. Double-precision floating point format was used for accuracy. Doses to the rectum, prostate, bladder and femoral heads were calculated. When running on a single GPU, the MC GPU code was found to be ×19 times faster than the CPU code and ×42 times faster than MCNPX. These speedup factors were doubled on the dual-GPU system. The dose Result was benchmarked against MCNPX and a maximum difference of 1% was observed when the relative error is kept below 0.1%. A GPU-based MC code was developed for dose calculations using detailed patient and CT scanner models. Efficiency and accuracy were both guaranteed in this code. Scalability of the code was confirmed on the dual-GPU system. © 2012 American Association of Physicists in Medicine.

Evaluation and application of the Baldwin-Lomax turbulence model in two-dimensional, unsteady, compressible boundary layers with and without separation in engine inlets

NASA Technical Reports Server (NTRS)

Sakowski, Barbara; Darling, Douglas; Roach, Robert L.; Vandewall, Allan

1992-01-01

There is a practical need to model high speed flows that exist in jet engine inlets. The boundary layers that form in these inlets may be turbulent or laminar and either separated or attached. Also, unsteady supersonic inlets may be subject to frequent changes in operating conditions. Some changes in the operating conditions of the inlets may include varying the inlet geometry, bleeds and bypasses, and rotating or translating the centerbody. In addition, the inlet may be either started or unstarted. Therefore, a CFD code, used to model these inlets, may have to run for several different cases. Also, since the flow conditions through an unsteady inlet may be continually fluctuating, the CFD code which models these flows may have to be run over many time steps. Therefore, it would be beneficial that the code run quickly. Many turbulence models, however, are cumbersome to implement and require a lot of computer time to run, since they add to the number of differential equations to be solved to model a flow. The Baldwin-Lomax turbulence model is a popular model. It is an algebraic, eddy viscosity model. The Baldwin-Lomax model is used in many CFD codes because it is quick and easy to implement. In this paper, we will discuss implementing the Baldwin-Lomax turbulence model for both steady and unsteady compressible flows. In addition, these flows may be either separated or attached. In order to apply this turbulence model to flows which may be subjected to these conditions, certain modifications should be made to the original Baldwin-Lomax model. We will discuss these modifications and determine whether the Baldwin-Lomax model is a viable turbulence model that produces reasonably accurate results for high speed flows that can be found in engine inlets.

Verification of the New FAST v8 Capabilities for the Modeling of Fixed-Bottom Offshore Wind Turbines: Preprint

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

Barahona, B.; Jonkman, J.; Damiani, R.

2014-12-01

Coupled dynamic analysis has an important role in the design of offshore wind turbines because the systems are subject to complex operating conditions from the combined action of waves and wind. The aero-hydro-servo-elastic tool FAST v8 is framed in a novel modularization scheme that facilitates such analysis. Here, we present the verification of new capabilities of FAST v8 to model fixed-bottom offshore wind turbines. We analyze a series of load cases with both wind and wave loads and compare the results against those from the previous international code comparison projects-the International Energy Agency (IEA) Wind Task 23 Subtask 2 Offshoremore » Code Comparison Collaboration (OC3) and the IEA Wind Task 30 OC3 Continued (OC4) projects. The verification is performed using the NREL 5-MW reference turbine supported by monopile, tripod, and jacket substructures. The substructure structural-dynamics models are built within the new SubDyn module of FAST v8, which uses a linear finite-element beam model with Craig-Bampton dynamic system reduction. This allows the modal properties of the substructure to be synthesized and coupled to hydrodynamic loads and tower dynamics. The hydrodynamic loads are calculated using a new strip theory approach for multimember substructures in the updated HydroDyn module of FAST v8. These modules are linked to the rest of FAST through the new coupling scheme involving mapping between module-independent spatial discretizations and a numerically rigorous implicit solver. The results show that the new structural dynamics, hydrodynamics, and coupled solutions compare well to the results from the previous code comparison projects.« less

FY2017 Updates to the SAS4A/SASSYS-1 Safety Analysis Code

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

Fanning, T. H.

The SAS4A/SASSYS-1 safety analysis software is used to perform deterministic analysis of anticipated events as well as design-basis and beyond-design-basis accidents for advanced fast reactors. It plays a central role in the analysis of U.S. DOE conceptual designs, proposed test and demonstration reactors, and in domestic and international collaborations. This report summarizes the code development activities that have taken place during FY2017. Extensions to the void and cladding reactivity feedback models have been implemented, and Control System capabilities have been improved through a new virtual data acquisition system for plant state variables and an additional Block Signal for a variablemore » lag compensator to represent reactivity feedback for novel shutdown devices. Current code development and maintenance needs are also summarized in three key areas: software quality assurance, modeling improvements, and maintenance of related tools. With ongoing support, SAS4A/SASSYS-1 can continue to fulfill its growing role in fast reactor safety analysis and help solidify DOE’s leadership role in fast reactor safety both domestically and in international collaborations.« less

Construction of type-II QC-LDPC codes with fast encoding based on perfect cyclic difference sets

NASA Astrophysics Data System (ADS)

Li, Ling-xiang; Li, Hai-bing; Li, Ji-bi; Jiang, Hua

2017-09-01

In view of the problems that the encoding complexity of quasi-cyclic low-density parity-check (QC-LDPC) codes is high and the minimum distance is not large enough which leads to the degradation of the error-correction performance, the new irregular type-II QC-LDPC codes based on perfect cyclic difference sets (CDSs) are constructed. The parity check matrices of these type-II QC-LDPC codes consist of the zero matrices with weight of 0, the circulant permutation matrices (CPMs) with weight of 1 and the circulant matrices with weight of 2 (W2CMs). The introduction of W2CMs in parity check matrices makes it possible to achieve the larger minimum distance which can improve the error- correction performance of the codes. The Tanner graphs of these codes have no girth-4, thus they have the excellent decoding convergence characteristics. In addition, because the parity check matrices have the quasi-dual diagonal structure, the fast encoding algorithm can reduce the encoding complexity effectively. Simulation results show that the new type-II QC-LDPC codes can achieve a more excellent error-correction performance and have no error floor phenomenon over the additive white Gaussian noise (AWGN) channel with sum-product algorithm (SPA) iterative decoding.

Dynamic performance of a suspended reinforced concrete footbridge under pedestrian movements

NASA Astrophysics Data System (ADS)

Drygala, I.; Dulinska, J.; Kondrat, K.

2018-02-01

In the paper the dynamic analysis of a suspended reinforced concrete footbridge over a national road located in South Poland was carried out. Firstly, modes and values of natural frequencies of vibration of the structure were calculated. The results of the numerical modal investigation shown that the natural frequencies of the structure coincided with the frequency of human beings during motion steps (walking fast or running). Hence, to consider the comfort standards, the dynamic response of the footbridge to a runner dynamic motion should be calculated. Secondly, the dynamic response of the footbridge was calculated taking into consideration two models of dynamic forces produced by a single running pedestrian: a ‘sine’ and ‘half-sine’ model. It occurred that the values of accelerations and displacements obtained for the ‘half-sine’ model of dynamic forces were greater than those obtained for the ‘sine’ model up 20%. The ‘sine’ model is appropriate only for walking users of the walkways, because the nature of their motion has continues characteristic. In the case of running users of walkways this theory is unfitting, since the forces produced by a running pedestrian has a discontinuous nature. In this scenario of calculations, a ‘half-sine’ model seemed to be more effective. Finally, the comfort conditions for the footbridge were evaluated. The analysis proved that the vertical comfort criteria were not exceeded for a single user of footbridge running or walking fast.

A Hybrid Constraint Representation and Reasoning Framework

NASA Technical Reports Server (NTRS)

Golden, Keith; Pang, Wan-Lin

2003-01-01

This paper introduces JNET, a novel constraint representation and reasoning framework that supports procedural constraints and constraint attachments, providing a flexible way of integrating the constraint reasoner with a run- time software environment. Attachments in JNET are constraints over arbitrary Java objects, which are defined using Java code, at runtime, with no changes to the JNET source code.

Codes, Costs, and Critiques: The Organization of Information in "Library Quarterly", 1931-2004

ERIC Educational Resources Information Center

Olson, Hope A.

2006-01-01

This article reports the results of a quantitative and thematic content analysis of the organization of information literature in the "Library Quarterly" ("LQ") between its inception in 1931 and 2004. The majority of articles in this category were published in the first half of "LQ's" run. Prominent themes have included cataloging codes and the…

Code-Switching Functions in Modern Hebrew Teaching and Learning

ERIC Educational Resources Information Center

Gilead, Yona

2016-01-01

The teaching and learning of Modern Hebrew outside of Israel is essential to Jewish education and identity. One of the most contested issues in Modern Hebrew pedagogy is the use of code-switching between Modern Hebrew and learners' first language. Moreover, this is one of the longest running disputes in the broader field of second language…

GPULife

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

Kelly, Priscilla N.

2016-08-12

The code runs the Game of Life among several processors. Each processor uses CUDA to set up the grid's buffer on the GPU, and that buffer is fed to other GPU languages to apply the rules of the game of life. Only the halo is copied off the buffer and exchanged using MPI. This code looks at the interoperability of GPU languages among current platforms.

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

Predictors of race time in male Ironman triathletes: physical characteristics, training, or prerace experience?

PubMed

Knechtle, Beat; Wirth, Andrea; Rosemann, Thomas

2010-10-01

The aim of the present study was to assess whether physical characteristics, training, or prerace experience were related to performance in recreational male Ironman triathletes using bi- and multivariate analysis. 83 male recreational triathletes who volunteered to participate in the study (M age 41.5 yr., SD = 8.9) had a mean body height of 1.80 m (SD = 0.06), mean body mass of 77.3 kg (SD = 8.9), and mean Body Mass Index of 23.7 kg/m2 (SD = 2.1) at the 2009 IRONMAN SWITZERLAND competition. Speed in running during training, personal best marathon time, and personal best time in an Olympic distance triathlon were related to the Ironman race time. These three variables explained 64% of the variance in Ironman race time. Personal best marathon time was significantly and positively related to the run split time in the Ironman race. Faster running while training and both a fast personal best time in a marathon and in an Olympic distance triathlon were associated with a fast Ironman race time.

CubiCal: Suite for fast radio interferometric calibration

NASA Astrophysics Data System (ADS)

Kenyon, J. S.; Smirnov, O. M.; Grobler, T. L.; Perkins, S. J.

2018-05-01

CubiCal implements several accelerated gain solvers which exploit complex optimization for fast radio interferometric gain calibration. The code can be used for both direction-independent and direction-dependent self-calibration. CubiCal is implemented in Python and Cython, and multiprocessing is fully supported.

TAIR- TRANSONIC AIRFOIL ANALYSIS COMPUTER CODE

NASA Technical Reports Server (NTRS)

Dougherty, F. C.

1994-01-01

The Transonic Airfoil analysis computer code, TAIR, was developed to employ a fast, fully implicit algorithm to solve the conservative full-potential equation for the steady transonic flow field about an arbitrary airfoil immersed in a subsonic free stream. The full-potential formulation is considered exact under the assumptions of irrotational, isentropic, and inviscid flow. These assumptions are valid for a wide range of practical transonic flows typical of modern aircraft cruise conditions. The primary features of TAIR include: a new fully implicit iteration scheme which is typically many times faster than classical successive line overrelaxation algorithms; a new, reliable artifical density spatial differencing scheme treating the conservative form of the full-potential equation; and a numerical mapping procedure capable of generating curvilinear, body-fitted finite-difference grids about arbitrary airfoil geometries. Three aspects emphasized during the development of the TAIR code were reliability, simplicity, and speed. The reliability of TAIR comes from two sources: the new algorithm employed and the implementation of effective convergence monitoring logic. TAIR achieves ease of use by employing a "default mode" that greatly simplifies code operation, especially by inexperienced users, and many useful options including: several airfoil-geometry input options, flexible user controls over program output, and a multiple solution capability. The speed of the TAIR code is attributed to the new algorithm and the manner in which it has been implemented. Input to the TAIR program consists of airfoil coordinates, aerodynamic and flow-field convergence parameters, and geometric and grid convergence parameters. The airfoil coordinates for many airfoil shapes can be generated in TAIR from just a few input parameters. Most of the other input parameters have default values which allow the user to run an analysis in the default mode by specifing only a few input parameters. Output from TAIR may include aerodynamic coefficients, the airfoil surface solution, convergence histories, and printer plots of Mach number and density contour maps. The TAIR program is written in FORTRAN IV for batch execution and has been implemented on a CDC 7600 computer with a central memory requirement of approximately 155K (octal) of 60 bit words. The TAIR program was developed in 1981.

Variability of segment coordination using a vector coding technique: Reliability analysis for treadmill walking and running.

PubMed

Hafer, Jocelyn F; Boyer, Katherine A

2017-01-01

Coordination variability (CV) quantifies the variety of movement patterns an individual uses during a task and may provide a measure of the flexibility of that individual's motor system. While there is growing popularity of segment CV as a marker of motor system health or adaptability, it is not known how many strides of data are needed to reliably calculate CV. This study aimed to determine the number of strides needed to reliably calculate CV in treadmill walking and running, and to compare CV between walking and running in a healthy population. Ten healthy young adults walked and ran at preferred speeds on a treadmill and a modified vector coding technique was used to calculate CV for the following segment couples: pelvis frontal plane vs. thigh frontal plane, thigh sagittal plane vs. shank sagittal plane, thigh sagittal plane vs. shank transverse plane, and shank transverse plane vs. rearfoot frontal plane. CV for each coupling of interest was calculated for 2-15 strides for each participant and gait type. Mean CV was calculated across the entire gait cycle and, separately, for 4 phases of the gait cycle. For running and walking 8 and 10 strides, respectively, were sufficient to obtain a reliable CV estimate. CV was significantly different between walking and running for the thigh vs. shank couple comparisons. These results suggest that 10 strides of treadmill data are needed to reliably calculate CV for walking and running. Additionally, the differences in CV between walking and running suggest that the role of knee (i.e., inter-thigh- shank) control may differ between these forms of locomotion. Copyright © 2016 Elsevier B.V. All rights reserved.

NONMEMory: a run management tool for NONMEM.

PubMed

Wilkins, Justin J

2005-06-01

NONMEM is an extremely powerful tool for nonlinear mixed-effect modelling and simulation of pharmacokinetic and pharmacodynamic data. However, it is a console-based application whose output does not lend itself to rapid interpretation or efficient management. NONMEMory has been created to be a comprehensive project manager for NONMEM, providing detailed summary, comparison and overview of the runs comprising a given project, including the display of output data, simple post-run processing, fast diagnostic plots and run output management, complementary to other available modelling aids. Analysis time ought not to be spent on trivial tasks, and NONMEMory's role is to eliminate these as far as possible by increasing the efficiency of the modelling process. NONMEMory is freely available from http://www.uct.ac.za/depts/pha/nonmemory.php.

Hardware requirements: A new generation partial reflection radar for studies of the equatorial mesosphere

NASA Technical Reports Server (NTRS)

Vincent, R. A.

1986-01-01

A new partial reflection (PR) radar is being developed for operation at the proposed Equatorial Observatory. The system is being designed to make maximum use of recent advances in solid-state technology in order to minimize the power requirements. In particular, it is planned to use a solid-state transmitter in place of the tube transmitters previously used in PR systems. Solid-state transmitters have the advantages that they do not need high voltage supplies, they do not require cathode heaters with a corresponding saving in power consumption and parts are readily available and inexpensive. It should be possible to achieve 15 kW peak powers with recently announced fast switching transistors. Since high mean powers are desirable for obtaining good signal-to-noise ratios, it is also planned to phase code the transmitted pulses and decode after coherent integration. All decoding and signal processing will be carried out in dedicated microprocessors before the signals are passed to a microcomputer for on-line analysis. Recent tests have shown that an Olivetti M24 micro (an IBM compatible) running an 8-MHz clock with a 8087 coprocessor can analyze data at least as fast as the minicomputers presently being used with the Adelaide PR rad ar and at a significantly lower cost. The processed winds data will be stored in nonvolatile CMOS RAM modules; about 0.5 to 1 Mbyte is required to store one week's information.

UBAT of UFFO/ Lomonosov: The X-Ray Space Telescope to Observe Early Photons from Gamma-Ray Bursts

NASA Astrophysics Data System (ADS)

Jeong, S.; Panasyuk, M. I.; Reglero, V.; Connell, P.; Kim, M. B.; Lee, J.; Rodrigo, J. M.; Ripa, J.; Eyles, C.; Lim, H.; Gaikov, G.; Jeong, H.; Leonov, V.; Chen, P.; Castro-Tirado, A. J.; Nam, J. W.; Svertilov, S.; Yashin, I.; Garipov, G.; Huang, M.-H. A.; Huang, J.-J.; Kim, J. E.; Liu, T.-C.; Petrov, V.; Bogomolov, V.; Budtz-Jørgensen, C.; Brandt, S.; Park, I. H.

2018-02-01

The Ultra-Fast Flash Observatory (UFFO) Burst Alert and Trigger Telescope (UBAT) has been designed and built for the localization of transient X-ray sources such as Gamma Ray Bursts (GRBs). As one of main instruments in the UFFO payload onboard the Lomonosov satellite (hereafter UFFO/ Lomonosov), the UBAT's roles are to monitor the X-ray sky, to rapidly locate and track transient sources, and to trigger the slewing of a UV/optical telescope, namely Slewing Mirror Telescope (SMT). The SMT, a pioneering application of rapid slewing mirror technology has a line of sight parallel to the UBAT, allowing us to measure the early UV/optical GRB counterpart and study the extremely early moments of GRB evolution. To detect X-rays, the UBAT utilizes a 191.1 cm2 scintillation detector composed of Yttrium Oxyorthosilicate (YSO) crystals, Multi-Anode Photomultiplier Tubes (MAPMTs), and associated electronics. To estimate a direction vector of a GRB source in its field of view, it employs the well-known coded aperture mask technique. All functions are written for implementation on a field programmable gate array to enable fast triggering and to run the device's imaging algorithms. The UFFO/ Lomonosov satellite was launched on April 28, 2016, and is now collecting GRB observation data. In this study, we describe the UBAT's design, fabrication, integration, and performance as a GRB X-ray trigger and localization telescope, both on the ground and in space.

Energy-Containing Length Scale at the Base of a Coronal Hole: New Observational Findings

NASA Astrophysics Data System (ADS)

Abramenko, V.; Dosch, A.; Zank, G. P.; Yurchyshyn, V.; Goode, P. R.

2012-12-01

Dynamics of the photospheric flux tubes is thought to be a key factor for generation and propagation of MHD waves and magnetic stress into the corona. Recently, New Solar Telescope (NST, Big Bear Solar Observatory) imaging observations in helium I 10830 Å revealed ultrafine, hot magnetic loops reaching from the photosphere to the corona and originating from intense, compact magnetic field elements. One of the essential input parameters to run the models of the fast solar wind is a characteristic energy-containing length scale, lambda, of the dynamical structures transverse to the mean magnetic field in a coronal hole (CH) in the base of the corona. We used NST time series of solar granulation motions to estimate the velocity fluctuations, as well as NST near-infrared magnetograms to derive the magnetic field fluctuations. The NST adaptive optics corrected speckle-reconstructed images of 10 seconds cadence were an input for the local correlation tracking (LCT) code to derive the squared transverse velocity patterns. We found that the characteristic length scale for the energy-carrying structures in the photosphere is about 300 km, which is two orders of magnitude lower than it was adopted in previous models. The influence of the result on the coronal heating and fast solar wind modeling will be discussed.; Correlation functions calculated from the squared velocities for the three data sets: a coronal hole, quiet sun and active region plage area.

ROSSTEP v1.3

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

Allevato, Adam

2016-07-21

ROSSTEP is a system for sequentially running roslaunch, rosnode, and bash scripts automatically, for use in Robot Operating System (ROS) applications. The system consists of YAML files which define actions and conditions. A python file parses the code and runs actions sequentially using the sys and subprocess python modules. Between actions, it uses various ROS-based code to check conditions required to proceed, and only moves on to the next action when all the necessary conditions have been met. Included is rosstep-creator, a QT application designed to create the YAML files required for ROSSTEP. It has a nearly one-to-one mapping frommore » interface elements to YAML output, and serves as a convenient GUI for working with the ROSSTEP system.« less

50 GFlops molecular dynamics on the Connection Machine 5

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

Lomdahl, P.S.; Tamayo, P.; Groenbech-Jensen, N.

1993-12-31

The authors present timings and performance numbers for a new short range three dimensional (3D) molecular dynamics (MD) code, SPaSM, on the Connection Machine-5 (CM-5). They demonstrate that runs with more than 10{sup 8} particles are now possible on massively parallel MIMD computers. To the best of their knowledge this is at least an order of magnitude more particles than what has previously been reported. Typical production runs show sustained performance (including communication) in the range of 47--50 GFlops on a 1024 node CM-5 with vector units (VUs). The speed of the code scales linearly with the number of processorsmore » and with the number of particles and shows 95% parallel efficiency in the speedup.« less

NPSS Multidisciplinary Integration and Analysis

NASA Technical Reports Server (NTRS)

Hall, Edward J.; Rasche, Joseph; Simons, Todd A.; Hoyniak, Daniel

2006-01-01

The objective of this task was to enhance the capability of the Numerical Propulsion System Simulation (NPSS) by expanding its reach into the high-fidelity multidisciplinary analysis area. This task investigated numerical techniques to convert between cold static to hot running geometry of compressor blades. Numerical calculations of blade deformations were iteratively done with high fidelity flow simulations together with high fidelity structural analysis of the compressor blade. The flow simulations were performed with the Advanced Ducted Propfan Analysis (ADPAC) code, while structural analyses were performed with the ANSYS code. High fidelity analyses were used to evaluate the effects on performance of: variations in tip clearance, uncertainty in manufacturing tolerance, variable inlet guide vane scheduling, and the effects of rotational speed on the hot running geometry of the compressor blades.

Adaptive responses of GLUT-4 and citrate synthase in fast-twitch muscle of voluntary running rats

NASA Technical Reports Server (NTRS)

Henriksen, E. J.; Halseth, A. E.

1995-01-01

Glucose transporter (GLUT-4) protein, hexokinase, and citrate synthase (proteins involved in oxidative energy production from blood glucose catabolism) increase in response to chronically elevated neuromuscular activity. It is currently unclear whether these proteins increase in a coordinated manner in response to this stimulus. Therefore, voluntary wheel running (WR) was used to chronically overload the fast-twitch rat plantaris muscle and the myocardium, and the early time courses of adaptative responses of GLUT-4 protein and the activities of hexokinase and citrate synthase were characterized and compared. Plantaris hexokinase activity increased 51% after just 1 wk of WR, whereas GLUT-4 and citrate synthase were increased by 51 and 40%, respectively, only after 2 wk of WR. All three variables remained comparably elevated (+50-64%) through 4 wk of WR. Despite the overload of the myocardium with this protocol, no substantial elevations in these variables were observed. These findings are consistent with a coordinated upregulation of GLUT-4 and citrate synthase in the fast-twitch plantaris, but not in the myocardium, in response to this increased neuromuscular activity. Regulation of hexokinase in fast-twitch muscle appears to be uncoupled from regulation of GLUT-4 and citrate synthase, as increases in the former are detectable well before increases in the latter.

A numerical model for dynamic wave rotor analysis

NASA Technical Reports Server (NTRS)

Paxson, D. E.

1995-01-01

A numerical model has been developed which can predict the dynamic (and steady state) performance of a wave rotor, given the geometry and time dependent boundary conditions. The one-dimensional, perfect gas, CFD based code tracks the gasdynamics in each of the wave rotor passages as they rotate past the various ducts. The model can operate both on and off-design, allowing dynamic behavior to be studied throughout the operating range of the wave rotor. The model accounts for several major loss mechanisms including finite passage opening time, fluid friction, heat transfer to and from the passage walls, and leakage to and from the passage ends. In addition, it can calculate the amount of work transferred to and from the fluid when the flow in the ducts is not aligned with the passages such as occurs in off-design operation. Since it is one-dimensional, the model runs reasonably fast on a typical workstation. This paper will describe the model and present the results of some transient calculations for a conceptual four port wave rotor designed as a topping cycle for a small gas turbine engine.

ShareSync: A Solution for Deterministic Data Sharing over Ethernet

NASA Technical Reports Server (NTRS)

Dunn, Daniel J., II; Koons, William A.; Kennedy, Richard D.; Davis, Philip A.

2007-01-01

As part of upgrading the Contact Dynamics Simulation Laboratory (CDSL) at the NASA Marshall Space Flight Center (MSFC), a simple, cost effective method was needed to communicate data among the networked simulation machines and I/O controllers used to run the facility. To fill this need and similar applicable situations, a generic protocol was developed, called ShareSync. ShareSync is a lightweight, real-time, publish-subscribe Ethernet protocol for simple and deterministic data sharing across diverse machines and operating systems. ShareSync provides a simple Application Programming Interface (API) for simulation programmers to incorporate into their code. The protocol is compatible with virtually all Ethernet-capable machines, is flexible enough to support a variety of applications, is fast enough to provide soft real-time determinism, and is a low-cost resource for distributed simulation development, deployment, and maintenance. The first design cycle iteration of ShareSync has been completed, and the protocol has undergone several testing procedures including endurance and benchmarking tests and approaches the 2001ts data synchronization design goal for the CDSL.

Multigrid direct numerical simulation of the whole process of flow transition in 3-D boundary layers

NASA Technical Reports Server (NTRS)

Liu, Chaoqun; Liu, Zhining

1993-01-01

A new technology was developed in this study which provides a successful numerical simulation of the whole process of flow transition in 3-D boundary layers, including linear growth, secondary instability, breakdown, and transition at relatively low CPU cost. Most other spatial numerical simulations require high CPU cost and blow up at the stage of flow breakdown. A fourth-order finite difference scheme on stretched and staggered grids, a fully implicit time marching technique, a semi-coarsening multigrid based on the so-called approximate line-box relaxation, and a buffer domain for the outflow boundary conditions were all used for high-order accuracy, good stability, and fast convergence. A new fine-coarse-fine grid mapping technique was developed to keep the code running after the laminar flow breaks down. The computational results are in good agreement with linear stability theory, secondary instability theory, and some experiments. The cost for a typical case with 162 x 34 x 34 grid is around 2 CRAY-YMP CPU hours for 10 T-S periods.

Steady flow model user's guide

NASA Astrophysics Data System (ADS)

Doughty, C.; Hellstrom, G.; Tsang, C. F.; Claesson, J.

1984-07-01

Sophisticated numerical models that solve the coupled mass and energy transport equations for nonisothermal fluid flow in a porous medium were used to match analytical results and field data for aquifer thermal energy storage (ATES) systems. As an alternative to the ATES problem the Steady Flow Model (SFM), a simplified but fast numerical model was developed. A steady purely radial flow field is prescribed in the aquifer, and incorporated into the heat transport equation which is then solved numerically. While the radial flow assumption limits the range of ATES systems that can be studied using the SFM, it greatly simplifies use of this code. The preparation of input is quite simple compared to that for a sophisticated coupled mass and energy model, and the cost of running the SFM is far cheaper. The simple flow field allows use of a special calculational mesh that eliminates the numerical dispersion usually associated with the numerical solution of convection problems. The problem is defined, the algorithm used to solve it are outllined, and the input and output for the SFM is described.

WinPSSP : a revamp of the computer program PSSP and its performance solving the crystal structures of small organic compounds and solids of biological and pharmaceutical interest

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

Pagola, Silvina; Polymeros, Alekos; Kourkoumelis, Nikolaos

2017-02-01

The direct-space methods softwarePowder Structure Solution Program(PSSP) [Pagola & Stephens (2010).J. Appl. Cryst.43, 370–376] has been migrated to the Windows OS and the code has been optimized for fast runs.WinPSSPis a user-friendly graphical user interface that allows the input of preliminary crystal structure information, integrated intensities of the reflections and FWHM, the definition of structural parameters and a simulated annealing schedule, and the visualization of the calculated and experimental diffraction data overlaid for each individual solution. The solutions are reported as filename.cif files, which can be used to analyze packing motifs and chemical bonding, and to input the atomic coordinatesmore » into the Rietveld analysis softwareGSAS. WinPSSPperformance in straightforward crystal structure determinations has been evaluated using 18 molecular solids with 6–20 degrees of freedom. The free-distribution program as well as multimedia tutorials can be accessed at http://users.uoi.gr/nkourkou/winpssp/.« less

A finite element code for electric motor design

NASA Technical Reports Server (NTRS)

Campbell, C. Warren

1994-01-01

FEMOT is a finite element program for solving the nonlinear magnetostatic problem. This version uses nonlinear, Newton first order elements. The code can be used for electric motor design and analysis. FEMOT can be embedded within an optimization code that will vary nodal coordinates to optimize the motor design. The output from FEMOT can be used to determine motor back EMF, torque, cogging, and magnet saturation. It will run on a PC and will be available to anyone who wants to use it.

The SIFT hardware/software systems. Volume 2: Software listings

NASA Technical Reports Server (NTRS)

Palumbo, Daniel L.

1985-01-01

This document contains software listings of the SIFT operating system and application software. The software is coded for the most part in a variant of the Pascal language, Pascal*. Pascal* is a cross-compiler running on the VAX and Eclipse computers. The output of Pascal* is BDX-390 assembler code. When necessary, modules are written directly in BDX-390 assembler code. The listings in this document supplement the description of the SIFT system found in Volume 1 of this report, A Detailed Description.

Instruct coders' manual

NASA Technical Reports Server (NTRS)

Friend, J.

1971-01-01

A manual designed both as an instructional manual for beginning coders and as a reference manual for the coding language INSTRUCT, is presented. The manual includes the major programs necessary to implement the teaching system and lists the limitation of current implementation. A detailed description is given of how to code a lesson, what buttons to push, and what utility programs to use. Suggestions for debugging coded lessons and the error messages that may be received during assembly or while running the lesson are given.

The SENSEI Generic In Situ Interface

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

Ayachit, Utkarsh; Whitlock, Brad; Wolf, Matthew

The SENSEI generic in situ interface is an API that promotes code portability and reusability. From the simulation view, a developer can instrument their code with the SENSEI API and then make make use of any number of in situ infrastructures. From the method view, a developer can write an in situ method using the SENSEI API, then expect it to run in any number of in situ infrastructures, or be invoked directly from a simulation code, with little or no modification. This paper presents the design principles underlying the SENSEI generic interface, along with some simplified coding examples.

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.

Domain Specific Language Support for Exascale. Final Project Report

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

Baden, Scott

The project developed a domain specific translator enable legacy MPI source code to tolerate communication delays, which are increasing over time due to technological factors. The translator performs source-to-source translation that incorporates semantic information into the translation process. The output of the translator is a C program runs as a data driven program, and uses an existing run time to overlap communication automatically

Program Synthesizes UML Sequence Diagrams

NASA Technical Reports Server (NTRS)

Barry, Matthew R.; Osborne, Richard N.

2006-01-01

A computer program called "Rational Sequence" generates Universal Modeling Language (UML) sequence diagrams of a target Java program running on a Java virtual machine (JVM). Rational Sequence thereby performs a reverse engineering function that aids in the design documentation of the target Java program. Whereas previously, the construction of sequence diagrams was a tedious manual process, Rational Sequence generates UML sequence diagrams automatically from the running Java code.

Resilient Diffusive Clouds

DTIC Science & Technology

2017-02-01

scale blade servers (Dell PowerEdge) [20]. It must be recognized however, that the findings are distributed over this collection of architectures not...current operating system designs run into millions of lines of code. Moreover, they compound the opportunity for compromise by granting device drivers...properties (e.g. IP & MAC address) so as to invalidate an adversary’s surveillance data. The current running and bootstrapping instances of the micro

The Proteus Navier-Stokes code

NASA Technical Reports Server (NTRS)

Towne, Charles E.; Bui, Trong T.; Cavicchi, Richard H.; Conley, Julianne M.; Molls, Frank B.; Schwab, John R.

1992-01-01

An effort is currently underway at NASA Lewis to develop two- and three-dimensional Navier-Stokes codes, called Proteus, for aerospace propulsion applications. The emphasis in the development of Proteus is not algorithm development or research on numerical methods, but rather the development of the code itself. The objective is to develop codes that are user-oriented, easily-modified, and well-documented. Well-proven, state-of-the-art solution algorithms are being used. Code readability, documentation (both internal and external), and validation are being emphasized. This paper is a status report on the Proteus development effort. The analysis and solution procedure are described briefly, and the various features in the code are summarized. The results from some of the validation cases that have been run are presented for both the two- and three-dimensional codes.

Real-time visual simulation of APT system based on RTW and Vega

NASA Astrophysics Data System (ADS)

Xiong, Shuai; Fu, Chengyu; Tang, Tao

2012-10-01

The Matlab/Simulink simulation model of APT (acquisition, pointing and tracking) system is analyzed and established. Then the model's C code which can be used for real-time simulation is generated by RTW (Real-Time Workshop). Practical experiments show, the simulation result of running the C code is the same as running the Simulink model directly in the Matlab environment. MultiGen-Vega is a real-time 3D scene simulation software system. With it and OpenGL, the APT scene simulation platform is developed and used to render and display the virtual scenes of the APT system. To add some necessary graphics effects to the virtual scenes real-time, GLSL (OpenGL Shading Language) shaders are used based on programmable GPU. By calling the C code, the scene simulation platform can adjust the system parameters on-line and get APT system's real-time simulation data to drive the scenes. Practical application shows that this visual simulation platform has high efficiency, low charge and good simulation effect.

Prediction of sound radiated from different practical jet engine inlets

NASA Technical Reports Server (NTRS)

Zinn, B. T.; Meyer, W. L.

1980-01-01

Existing computer codes for calculating the far field radiation patterns surrounding various practical jet engine inlet configurations under different excitation conditions were upgraded. The computer codes were refined and expanded so that they are now more efficient computationally by a factor of about three and they are now capable of producing accurate results up to nondimensional wave numbers of twenty. Computer programs were also developed to help generate accurate geometrical representations of the inlets to be investigated. This data is required as input for the computer programs which calculate the sound fields. This new geometry generating computer program considerably reduces the time required to generate the input data which was one of the most time consuming steps in the process. The results of sample runs using the NASA-Lewis QCSEE inlet are presented and comparison of run times and accuracy are made between the old and upgraded computer codes. The overall accuracy of the computations is determined by comparison of the results of the computations with simple source solutions.

Euler technology assessment for preliminary aircraft design employing OVERFLOW code with multiblock structured-grid method

NASA Technical Reports Server (NTRS)

Treiber, David A.; Muilenburg, Dennis A.

1995-01-01

The viability of applying a state-of-the-art Euler code to calculate the aerodynamic forces and moments through maximum lift coefficient for a generic sharp-edge configuration is assessed. The OVERFLOW code, a method employing overset (Chimera) grids, was used to conduct mesh refinement studies, a wind-tunnel wall sensitivity study, and a 22-run computational matrix of flow conditions, including sideslip runs and geometry variations. The subject configuration was a generic wing-body-tail geometry with chined forebody, swept wing leading-edge, and deflected part-span leading-edge flap. The analysis showed that the Euler method is adequate for capturing some of the non-linear aerodynamic effects resulting from leading-edge and forebody vortices produced at high angle-of-attack through C(sub Lmax). Computed forces and moments, as well as surface pressures, match well enough useful preliminary design information to be extracted. Vortex burst effects and vortex interactions with the configuration are also investigated.

Billing and coding knowledge: a comparative survey of professional coders, practicing orthopedic surgeons, and orthopedic residents.

PubMed

Wiley, Kevin F; Yousuf, Tariq; Pasque, Charles B; Yousuf, Khalid

2014-06-01

Medical knowledge and surgical skills are necessary to become an effective orthopedic surgeon. To run an efficient practice, the surgeon must also possess a basic understanding of medical business practices, including billing and coding. In this study, we surveyed and compared the level of billing and coding knowledge among current orthopedic residents PGY3 and higher, academic and private practice attending orthopedic surgeons, and orthopedic coding professionals. According to the survey results, residents and fellows have a similar knowledge of coding and billing, regardless of their level of training or type of business education received in residency. Most residents would like formal training in coding, billing, and practice management didactics; this is consistent with data from previous studies.

Development of a Run Time Math Library for the 1750A Airborne Microcomputer.

DTIC Science & Technology

1985-12-01

premiue CWUTLDK Is R: Integer :a 0; 0: Integer :ul; LNMM: UEM; -Compute the Lado (alpii) for J In 0..Ol.K-1) loop Itf 0(14 1)/ 0. 0...ORGANIZATION (If appiicable) * School of Engineering AFIT/ ENC 6c. ADDRESS (City, State and ZIP Code) 7b. ADDRESS (City. State and ZIP Code) Air Force

Adoption of Test Driven Development and Continuous Integration for the Development of the Trick Simulation Toolkit

NASA Technical Reports Server (NTRS)

Penn, John M.

2013-01-01

This paper describes the adoption of a Test Driven Development approach and a Continuous Integration System in the development of the Trick Simulation Toolkit, a generic simulation development environment for creating high fidelity training and engineering simulations at the NASA/Johnson Space Center and many other NASA facilities. It describes what was learned and the significant benefits seen, such as fast, thorough, and clear test feedback every time code is checked-in to the code repository. It also describes a system that encourages development of code that is much more flexible, maintainable, and reliable. The Trick Simulation Toolkit development environment provides a common architecture for user-defined simulations. Trick builds executable simulations using user-supplied simulation-definition files (S_define) and user supplied "model code". For each Trick-based simulation, Trick automatically provides job scheduling, checkpoint / restore, data-recording, interactive variable manipulation (variable server), and an input-processor. Also included are tools for plotting recorded data and various other supporting tools and libraries. Trick is written in C/C++ and Java and supports both Linux and MacOSX. Prior to adopting this new development approach, Trick testing consisted primarily of running a few large simulations, with the hope that their complexity and scale would exercise most of Trick's code and expose any recently introduced bugs. Unsurprising, this approach yielded inconsistent results. It was obvious that a more systematic, thorough approach was required. After seeing examples of some Java-based projects that used the JUnit test framework, similar test frameworks for C and C++ were sought. Several were found, all clearly inspired by JUnit. Googletest, a freely available Open source testing framework, was selected as the most appropriate and capable. The new approach was implemented while rewriting the Trick memory management component, to eliminate a fundamental design flaw. The benefits became obvious almost immediately, not just in the correctness of the individual functions and classes but also in the correctness and flexibility being added to the overall design. Creating code to be testable, and testing as it was created resulted not only in better working code, but also in better-organized, flexible, and readable (i.e., articulate) code. This was, in essence the Test-driven development (TDD) methodology created by Kent Beck. Seeing the benefits of Test Driven Development, other Trick components were refactored to make them more testable and tests were designed and implemented for them.

Simulated Raman Spectral Analysis of Organic Molecules

NASA Astrophysics Data System (ADS)

Lu, Lu

The advent of the laser technology in the 1960s solved the main difficulty of Raman spectroscopy, resulted in simplified Raman spectroscopy instruments and also boosted the sensitivity of the technique. Up till now, Raman spectroscopy is commonly used in chemistry and biology. As vibrational information is specific to the chemical bonds, Raman spectroscopy provides fingerprints to identify the type of molecules in the sample. In this thesis, we simulate the Raman Spectrum of organic and inorganic materials by General Atomic and Molecular Electronic Structure System (GAMESS) and Gaussian, two computational codes that perform several general chemistry calculations. We run these codes on our CPU-based high-performance cluster (HPC). Through the message passing interface (MPI), a standardized and portable message-passing system which can make the codes run in parallel, we are able to decrease the amount of time for computation and increase the sizes and capacities of systems simulated by the codes. From our simulations, we will set up a database that allows search algorithm to quickly identify N-H and O-H bonds in different materials. Our ultimate goal is to analyze and identify the spectra of organic matter compositions from meteorites and compared these spectra with terrestrial biologically-produced amino acids and residues.

A C Language Implementation of the SRO (Murdock) Detector/Analyzer

USGS Publications Warehouse

Murdock, James N.; Halbert, Scott E.

1991-01-01

A signal detector and analyzer algorithm was described by Murdock and Hutt in 1983. The algorithm emulates the performance of a human interpreter of seismograms. It estimates the signal onset, the direction of onset (positive or negative), the quality of these determinations, the period and amplitude of the signal, and the background noise at the time of the signal. The algorithm has been coded in C language for implementation as a 'blackbox' for data similar to that of the China Digital Seismic Network. A driver for the algorithm is included, as are suggestions for other drivers. In all of these routines, plus several FIR filters that are included as well, floating point operations are not required. Multichannel operation is supported. Although the primary use of the code has been for in-house processing of broadband and short period data of the China Digital Seismic Network, provisions have been made to process the long period and very long period data of that system as well. The code for the in-house detector, which runs on a mini-computer, is very similar to that of the field system, which runs on a microprocessor. The code is documented.

SNPmplexViewer--toward a cost-effective traceability system

PubMed Central

2011-01-01

Background Beef traceability has become mandatory in many regions of the world and is typically achieved through the use of unique numerical codes on ear tags and animal passports. DNA-based traceability uses the animal's own DNA code to identify it and the products derived from it. Using SNaPshot, a primer-extension-based method, a multiplex of 25 SNPs in a single reaction has been practiced for reducing the expense of genotyping a panel of SNPs useful for identity control. Findings To further decrease SNaPshot's cost, we introduced the Perl script SNPmplexViewer, which facilitates the analysis of trace files for reactions performed without the use of fluorescent size standards. SNPmplexViewer automatically aligns reference and target trace electropherograms, run with and without fluorescent size standards, respectively. SNPmplexViewer produces a modified target trace file containing a normalised trace in which the reference size standards are embedded. SNPmplexViewer also outputs aligned images of the two electropherograms together with a difference profile. Conclusions Modified trace files generated by SNPmplexViewer enable genotyping of SnaPshot reactions performed without fluorescent size standards, using common fragment-sizing software packages. SNPmplexViewer's normalised output may also improve the genotyping software's performance. Thus, SNPmplexViewer is a general free tool enabling the reduction of SNaPshot's cost as well as the fast viewing and comparing of trace electropherograms for fragment analysis. SNPmplexViewer is available at http://cowry.agri.huji.ac.il/cgi-bin/SNPmplexViewer.cgi. PMID:21600063

Real-Time Motion Capture Toolbox (RTMocap): an open-source code for recording 3-D motion kinematics to study action-effect anticipations during motor and social interactions.

PubMed

Lewkowicz, Daniel; Delevoye-Turrell, Yvonne

2016-03-01

We present here a toolbox for the real-time motion capture of biological movements that runs in the cross-platform MATLAB environment (The MathWorks, Inc., Natick, MA). It provides instantaneous processing of the 3-D movement coordinates of up to 20 markers at a single instant. Available functions include (1) the setting of reference positions, areas, and trajectories of interest; (2) recording of the 3-D coordinates for each marker over the trial duration; and (3) the detection of events to use as triggers for external reinforcers (e.g., lights, sounds, or odors). Through fast online communication between the hardware controller and RTMocap, automatic trial selection is possible by means of either a preset or an adaptive criterion. Rapid preprocessing of signals is also provided, which includes artifact rejection, filtering, spline interpolation, and averaging. A key example is detailed, and three typical variations are developed (1) to provide a clear understanding of the importance of real-time control for 3-D motion in cognitive sciences and (2) to present users with simple lines of code that can be used as starting points for customizing experiments using the simple MATLAB syntax. RTMocap is freely available (http://sites.google.com/site/RTMocap/) under the GNU public license for noncommercial use and open-source development, together with sample data and extensive documentation.

Wavefront coding for fast, high-resolution light-sheet microscopy (Conference Presentation)

NASA Astrophysics Data System (ADS)

Olarte, Omar E.; Licea-Rodriguez, Jacob; Loza-Alvarez, Pablo

2017-02-01

Some biological experiments demand the observation of dynamics processes in 3D with high spatiotemporal resolution. The use of wavefront coding to extend the depth-of-field (DOF) of the collection arm of a light-sheet microscope is an interesting alternative for fast 3D imaging. Under this scheme, the 3D features of the sample are captured at high volumetric rates while the light sheet is swept rapidly within the extended DOF. The DOF is extended by coding the pupil function of the imaging lens by using a custom-designed phase mask. A posterior restoration step is required to decode the information of the captured images based on the applied phase mask [1]. This hybrid optical-digital approach is known as wavefront coding (WFC). Previously, we have demonstrated this method for performing fast 3D imaging of biological samples at medium resolution [2]. In this work, we present the extension of this approach for high-resolution microscopes. Under these conditions, the effective DOF of a standard high NA objective is of a few micrometers. Here we demonstrate that by the use of WFC, we can extend the DOF more than one order of magnitude keeping the high-resolution imaging. This is demonstrated for two designed phase masks using Zebrafish and C. elegans samples. [1] Olarte, O.E., Andilla, J., Artigas, D., and Loza-Alvarez, P., "Decoupled Illumination-Detection Microscopy. Selected Optics in Year 2105," in Optics and Photonics news 26, p. 41 (2015). [2] Olarte, O.E., Andilla, J., Artigas, D., and Loza-Alvarez, P., "Decoupled illumination detection in light sheet microscopy for fast volumetric imaging," Optica 2(8), 702 (2015).

A fast and high performance multiple data integration algorithm for identifying human disease genes

PubMed Central

2015-01-01

Background Integrating multiple data sources is indispensable in improving disease gene identification. It is not only due to the fact that disease genes associated with similar genetic diseases tend to lie close with each other in various biological networks, but also due to the fact that gene-disease associations are complex. Although various algorithms have been proposed to identify disease genes, their prediction performances and the computational time still should be further improved. Results In this study, we propose a fast and high performance multiple data integration algorithm for identifying human disease genes. A posterior probability of each candidate gene associated with individual diseases is calculated by using a Bayesian analysis method and a binary logistic regression model. Two prior probability estimation strategies and two feature vector construction methods are developed to test the performance of the proposed algorithm. Conclusions The proposed algorithm is not only generated predictions with high AUC scores, but also runs very fast. When only a single PPI network is employed, the AUC score is 0.769 by using F2 as feature vectors. The average running time for each leave-one-out experiment is only around 1.5 seconds. When three biological networks are integrated, the AUC score using F3 as feature vectors increases to 0.830, and the average running time for each leave-one-out experiment takes only about 12.54 seconds. It is better than many existing algorithms. PMID:26399620

Efficient convolutional sparse coding

DOEpatents

Wohlberg, Brendt

2017-06-20

Computationally efficient algorithms may be applied for fast dictionary learning solving the convolutional sparse coding problem in the Fourier domain. More specifically, efficient convolutional sparse coding may be derived within an alternating direction method of multipliers (ADMM) framework that utilizes fast Fourier transforms (FFT) to solve the main linear system in the frequency domain. Such algorithms may enable a significant reduction in computational cost over conventional approaches by implementing a linear solver for the most critical and computationally expensive component of the conventional iterative algorithm. The theoretical computational cost of the algorithm may be reduced from O(M.sup.3N) to O(MN log N), where N is the dimensionality of the data and M is the number of elements in the dictionary. This significant improvement in efficiency may greatly increase the range of problems that can practically be addressed via convolutional sparse representations.