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The impact of supercomputers on experimentation - A view from a National Laboratory

The relative roles of large-scale scientific computers and physical experiments in several science and engineering disciplines are discussed. Increasing dependence on computers is shown to be motivated both by the rapid growth in computer speed and memory, which permits accurate numerical simulation of complex physical phenomena, and by the rapid reduction in the cost of performing a calculation, which makes computation an increasingly attractive complement to experimentation. Computer speed and memory requirements are presented for selected areas of such disciplines as fluid dynamics, aerodynamics, aerothermodynamics, chemistry, atmospheric sciences, astronomy, and astrophysics, together with some examples of the complementary nature of computation and experiment. Finally, the impact of the emerging role of computers in the technical disciplines is discussed in terms of both the requirements for experimentation and the attainment of previously inaccessible information on physical processes.

Peterson, V. L.

The Impact of Supercomputers on Experimentation: A View from a National Laboratory

The relative roles of large-scale scientific computers and physical experiments in several science and engineering disciplines are discussed. Increasing dependence on computers is shown to be motivated both by the rapid growth in computer speed and memory, which permits accurate numerical simulation of complex physical phenomena, and by the rapid reduction in the cost of performing a calculation, which makes computation an increasingly, attractive complement to experimentation. Computer speed and memory requirements are presented for selected areas of such disciplines as fluid dynamics, aerodynamics, aerothermodynamics, chemistry, atmospheric sciences, astronomy, and astrophysics, together with some examples of the complementary nature of computation and experiment. Finally the impact of the emerging role of computers in the technical disciplines is discussed in terms of both the requirements for experimentation and the attainment of previously inaccessible information on physical processes.

Peterson, V.L.

FLAMES─Fast, Low-Storage, Accurate, and Memory-Efficient Adaptive Sampling─Approach to Resolve Spatially Dependent Dynamics of Molecular Liquids

Many critical phenomena in soft matter occur at large length scales, necessitating the resolution of their structure and dynamics at low wavenumbers. However, resolving wavenumber-dependent dynamics computationally via molecular dynamics simulations presents significant challenges, as these phenomena span several orders of magnitude in both time and length scales, resulting in high computational costs and memory demands. Here, this work highlights the computational and memory challenges associated with analyzing molecular trajectories in reciprocal space and demonstrates a method to address them. We introduce FLAMESFast, Low-storage, Accurate, and Memory-Efficient adaptive Sampling, which is a direct method for calculation of structure factors, allowing us to select only the required number of wavevectors for binning. We also use wavenumber-dependent time steps to extract dynamics. Our FLAMES approach effectively mitigates computational and memory/storage bottlenecks. We demonstrate the method using simulations of a model system, liquid octane, at various temperatures. Comparisons with experimental data and real space computation show that the FLAMES technique achieves high accuracy in resolving temperature- and spatially dependent dynamics while being significantly more computationally efficient and requiring less memory and storage than methods based on a uniform wavevector grid and fixed temporal spacing.

Chen, Guang [Argonne National Laboratory (ANL), Ar

The efficient calculation of chemically reacting flow

A semi-implicit finite volume formulation is used to study flows with chemical reactions. In this formulation the source terms resulting from the chemical reactions are treated implicitly and the resulting system of partial differential equations is solved using two time-stepping schemes. The first is based on the Runge-Kutta method while the second is based on an Adams predictor-corrector method. Results show that improvements in computational efficiency depend to a large extent on the manner in which the source term is treated. Further, analysis and computation indicate that the Runge-Kutta method is more efficient than the Adams methods. Finally, an adaptive time stepping scheme is developed to study problems involving shock ignition. Calculations for a hydrogen-air system agree well with other methods.

Eklund, D. R.

Development of an efficient computer code to solve the time-dependent Navier-Stokes equations

A research effort was conducted with the goal of reducing computer time of a Navier Stokes Computer Code for prediction of viscous flow fields about lifting bodies. A two-dimensional, time-dependent, laminar, transonic computer code (STOKES) was modified to incorporate a non-uniform timestep procedure. The non-uniform time-step requires updating of a zone only as often as required by its own stability criteria or that of its immediate neighbors. In the uniform timestep scheme each zone is updated as often as required by the least stable zone of the finite difference mesh. Because of less frequent update of program variables it was expected that the nonuniform timestep would result in a reduction of execution time by a factor of five to ten. Available funding was exhausted prior to successful demonstration of the benefits to be derived from the non-uniform time-step method.

Harp, J. L., Jr.

Provenance Challenges for Earth Science Dataset Publication

Modern science is increasingly dependent on computational analysis of very large data sets. Organizing, referencing, publishing those data has become a complex problem. Published research that depends on such data often fails to cite the data in sufficient detail to allow an independent scientist to reproduce the original experiments and analyses. This paper explores some of the challenges related to data identification, equivalence and reproducibility in the domain of data intensive scientific processing. It will use the example of Earth Science satellite data, but the challenges also apply to other domains.

Tilmes, Curt

Implicit hybrid schemes for the flux-difference split, three-dimensional Navier-Stokes equations

Implicit hybrid algorithms employing symmetric planar Gauss-Seidel (SPGS) relaxation and either block-tridiagonally structured coefficient matrices (AF-SPGS) or block-triangular coefficient matrices (LU-SPGS) are derived to solve the flux-difference-split Navier-Stokes equations for three-dimensional incompressible flow in an upwind scheme. The physical basis of the approach is discussed, and results for problems involving vortex flow around a thin delta wing at Reynolds numbers 900,000 and 10,000 are presented graphically. It is found that AF-SPGS converges faster on vector computers which depend on long vector lengths to achieve optimum performance, whereas LU-SPGS is preferable on sequentially operating machines and vector computers using shorter vector lengths.

Hartwich, P.-M.

Space-borne computing for the year 2000 and beyond

The influence and utilization of computers in space science investigations greatly enhances the ability to address difficult and complicated questions about the Universe. Space Science is wholly dependent on computers because the data acquired from instruments on the spacecraft are not only complicated in form but also voluminous. Athough a great deal of attention has been paid to develop efficient and powerful computing systems on-ground, research in the area of spaceborne computing is far from satisfactory. On-board processing of data will be important in future planetary missions where telemetry rates constrain the total amount of data which can be returned and decisions may have to be made in real time. Little thought has been given to a dynamic man-machine interface with regard to scientific real-time interactive control of flight experiments. Careful thinking is therefore essential to define appropriate spaceborne computing requirements for the future. It is imperative that powerful multiprocessing systems for on-board processing be experimentally impleneted and evaluated in selected application missions. The presentation addresses key issues and attempts to define the requirements for such processing with some of NASA's future missions in perspective. The resulting architectural and performance issues and possible developments are also addressed.

Iyer, Ravi K.

Applying Model-Based Reasoning to the FDIR of the Command and Data Handling Subsystem of the International Space Station

All of the International Space Station (ISS) systems which require computer control depend upon the hardware and software of the Command and Data Handling System (C&DH) system, currently a network of over 30 386-class computers called Multiplexor/Dimultiplexors (MDMs)[18]. The Caution and Warning System (C&W)[7], a set of software tasks that runs on the MDMs, is responsible for detecting, classifying, and reporting errors in all ISS subsystems including the C&DH. Fault Detection, Isolation and Recovery (FDIR) of these errors is typically handled with a combination of automatic and human effort. We are developing an Advanced Diagnostic System (ADS) to augment the C&W system with decision support tools to aid in root cause analysis as well as resolve differing human and machine C&DH state estimates. These tools which draw from sources in model-based reasoning[ 16,291, will improve the speed and accuracy of flight controllers by reducing the uncertainty in C&DH state estimation, allowing for a more complete assessment of risk. We have run tests with ISS telemetry and focus on those C&W events which relate to the C&DH system itself. This paper describes our initial results and subsequent plans.

Robinson, Peter

Chemical application of diffusion quantum Monte Carlo

The diffusion quantum Monte Carlo (QMC) method gives a stochastic solution to the Schroedinger equation. This approach is receiving increasing attention in chemical applications as a result of its high accuracy. However, reducing statistical uncertainty remains a priority because chemical effects are often obtained as small differences of large numbers. As an example, the single-triplet splitting of the energy of the methylene molecule CH sub 2 is given. The QMC algorithm was implemented on the CYBER 205, first as a direct transcription of the algorithm running on the VAX 11/780, and second by explicitly writing vector code for all loops longer than a crossover length C. The speed of the codes relative to one another as a function of C, and relative to the VAX, are discussed. The computational time dependence obtained versus the number of basis functions is discussed and this is compared with that obtained from traditional quantum chemistry codes and that obtained from traditional computer architectures.

Reynolds, P. J.

Highly Scalable Matching Pursuit Signal Decomposition Algorithm

Matching Pursuit Decomposition (MPD) is a powerful iterative algorithm for signal decomposition and feature extraction. MPD decomposes any signal into linear combinations of its dictionary elements or atoms . A best fit atom from an arbitrarily defined dictionary is determined through cross-correlation. The selected atom is subtracted from the signal and this procedure is repeated on the residual in the subsequent iterations until a stopping criterion is met. The reconstructed signal reveals the waveform structure of the original signal. However, a sufficiently large dictionary is required for an accurate reconstruction; this in return increases the computational burden of the algorithm, thus limiting its applicability and level of adoption. The purpose of this research is to improve the scalability and performance of the classical MPD algorithm. Correlation thresholds were defined to prune insignificant atoms from the dictionary. The Coarse-Fine Grids and Multiple Atom Extraction techniques were proposed to decrease the computational burden of the algorithm. The Coarse-Fine Grids method enabled the approximation and refinement of the parameters for the best fit atom. The ability to extract multiple atoms within a single iteration enhanced the effectiveness and efficiency of each iteration. These improvements were implemented to produce an improved Matching Pursuit Decomposition algorithm entitled MPD++. Disparate signal decomposition applications may require a particular emphasis of accuracy or computational efficiency. The prominence of the key signal features required for the proper signal classification dictates the level of accuracy necessary in the decomposition. The MPD++ algorithm may be easily adapted to accommodate the imposed requirements. Certain feature extraction applications may require rapid signal decomposition. The full potential of MPD++ may be utilized to produce incredible performance gains while extracting only slightly less energy than the standard algorithm. When the utmost accuracy must be achieved, the modified algorithm extracts atoms more conservatively but still exhibits computational gains over classical MPD. The MPD++ algorithm was demonstrated using an over-complete dictionary on real life data. Computational times were reduced by factors of 1.9 and 44 for the emphases of accuracy and performance, respectively. The modified algorithm extracted similar amounts of energy compared to classical MPD. The degree of the improvement in computational time depends on the complexity of the data, the initialization parameters, and the breadth of the dictionary. The results of the research confirm that the three modifications successfully improved the scalability and computational efficiency of the MPD algorithm. Correlation Thresholding decreased the time complexity by reducing the dictionary size. Multiple Atom Extraction also reduced the time complexity by decreasing the number of iterations required for a stopping criterion to be reached. The Course-Fine Grids technique enabled complicated atoms with numerous variable parameters to be effectively represented in the dictionary. Due to the nature of the three proposed modifications, they are capable of being stacked and have cumulative effects on the reduction of the time complexity.

Christensen, Daniel

Turbulence modeling and experiments

The best way of verifying turbulence is to do a direct comparison between the various terms and their models. The success of this approach depends upon the availability of the data for the exact correlations (both experimental and DNS). The other approach involves numerically solving the differential equations and then comparing the results with the data. The results of such a computation will depend upon the accuracy of all the modeled terms and constants. Because of this it is sometimes difficult to find the cause of a poor performance by a model. However, such a calculation is still meaningful in other ways as it shows how a complete Reynolds stress model performs. Thirteen homogeneous flows are numerically computed using the second order closure models. We concentrate only on those models which use a linear (or quasi-linear) model for the rapid term. This, therefore, includes the Launder, Reece and Rodi (LRR) model; the isotropization of production (IP) model; and the Speziale, Sarkar, and Gatski (SSG) model. Which of the three models performs better is examined along with what are their weaknesses, if any. The other work reported deal with the experimental balances of the second moment equations for a buoyant plume. Despite the tremendous amount of activity toward the second order closure modeling of turbulence, very little experimental information is available about the budgets of the second moment equations. Part of the problem stems from our inability to measure the pressure correlations. However, if everything else appearing in these equations is known from the experiment, pressure correlations can be obtained as the closing terms. This is the closest we can come to in obtaining these terms from experiment, and despite the measurement errors which might be present in such balances, the resulting information will be extremely useful for the turbulence modelers. The purpose of this part of the work was to provide such balances of the Reynolds stress and heat flux equations for the buoyant plume.

Shabbir, Aamir

Understanding the Scalability of Bayesian Network Inference Using Clique Tree Growth Curves

One of the main approaches to performing computation in Bayesian networks (BNs) is clique tree clustering and propagation. The clique tree approach consists of propagation in a clique tree compiled from a Bayesian network, and while it was introduced in the 1980s, there is still a lack of understanding of how clique tree computation time depends on variations in BN size and structure. In this article, we improve this understanding by developing an approach to characterizing clique tree growth as a function of parameters that can be computed in polynomial time from BNs, specifically: (i) the ratio of the number of a BN s non-root nodes to the number of root nodes, and (ii) the expected number of moral edges in their moral graphs. Analytically, we partition the set of cliques in a clique tree into different sets, and introduce a growth curve for the total size of each set. For the special case of bipartite BNs, there are two sets and two growth curves, a mixed clique growth curve and a root clique growth curve. In experiments, where random bipartite BNs generated using the BPART algorithm are studied, we systematically increase the out-degree of the root nodes in bipartite Bayesian networks, by increasing the number of leaf nodes. Surprisingly, root clique growth is well-approximated by Gompertz growth curves, an S-shaped family of curves that has previously been used to describe growth processes in biology, medicine, and neuroscience. We believe that this research improves the understanding of the scaling behavior of clique tree clustering for a certain class of Bayesian networks; presents an aid for trade-off studies of clique tree clustering using growth curves; and ultimately provides a foundation for benchmarking and developing improved BN inference and machine learning algorithms.

Mengshoel, Ole J.

Drag characteristics of unsteady, perturbed boundary layer flows

A series of time-dependent numerical computations have been performed for the flow of an unsteady boundary layer over an embedded cavity, which is aligned normal to the flow direction. The unsteady flow is the result of the imposition of a Stuart vortex, at the inflow boundary of the computational domain, onto an otherwise unperturbed two-dimensional laminar boundary layer flow. This produces a strongly vortical, but spatially monochromatic, motion at inflow which is allowed to evolve downstream through the time-dependent numerical solution of appropriate conservation equations. As the imposed vortex evolves over the solid boundary, a weaker induced vortical motion is produced and together these perturbing motions interact with the fluid motion in the embedded cavity. An analysis of the pertinent dynamic variables as well as the time-dependent drag characteristics for this type of non-planar geometry is performed; with particular emphasis on the relative contribution of both pressure drag and frictional drag at various times in the evolution process.

Gatski, T. B.

Methods and principles for determining task dependent interface content

Computer generated information displays provide a promising technology for offsetting the increasing complexity of the National Airspace System. To realize this promise, however, we must extend and adapt the domain-dependent knowledge that informally guides the design of traditional dedicated displays. In our view, the successful exploitation of computer generated displays revolves around the idea of information management, that is, the identification, organization, and presentation of relevant and timely information in a complex task environment. The program of research that is described leads to methods and principles for information management in the domain of commercial aviation. The multi-year objective of the proposed program of research is to develop methods and principles for determining task dependent interface content.

Shalin, Valerie L.

Experiences with Probabilistic Analysis Applied to Controlled Systems

This paper presents a semi-analytic method for computing frequency dependent means, variances, and failure probabilities for arbitrarily large-order closed-loop dynamical systems possessing a single uncertain parameter or with multiple highly correlated uncertain parameters. The approach will be shown to not suffer from the same computational challenges associated with computing failure probabilities using conventional FORM/SORM techniques. The approach is demonstrated by computing the probabilistic frequency domain performance of an optimal feed-forward disturbance rejection scheme.

Kenny, Sean P.

Bayesian Research at the NASA Ames Research Center,Computational Sciences Division

NASA Ames Research Center is one of NASA s oldest centers, having started out as part of the National Advisory Committee on Aeronautics, (NACA). The site, about 40 miles south of San Francisco, still houses many wind tunnels and other aviation related departments. In recent years, with the growing realization that space exploration is heavily dependent on computing and data analysis, its focus has turned more towards Information Technology. The Computational Sciences Division has expanded rapidly as a result. In this article, I will give a brief overview of some of the past and present projects with a Bayesian content. Much more than is described here goes on with the Division. The web pages at http://ic.arc. nasa.gov give more information on these, and the other Division projects.

Morris, Robin D.