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At least 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
NASA NTRS2001

Better, Cheaper, Faster Molecular Dynamics

Recent, revolutionary progress in genomics and structural, molecular and cellular biology has created new opportunities for molecular-level computer simulations of biological systems by providing vast amounts of data that require interpretation. These opportunities are further enhanced by the increasing availability of massively parallel computers. For many problems, the method of choice is classical molecular dynamics (iterative solving of Newton's equations of motion). It focuses on two main objectives. One is to calculate the relative stability of different states of the system. A typical problem that has' such an objective is computer-aided drug design. Another common objective is to describe evolution of the system towards a low energy (possibly the global minimum energy), "native" state. Perhaps the best example of such a problem is protein folding. Both types of problems share the same difficulty. Often, different states of the system are separated by high energy barriers, which implies that transitions between these states are rare events. This, in turn, can greatly impede exploration of phase space. In some instances this can lead to "quasi non-ergodicity", whereby a part of phase space is inaccessible on time scales of the simulation. To overcome this difficulty and to extend molecular dynamics to "biological" time scales (millisecond or longer) new physical formulations and new algorithmic developments are required. To be efficient they should account for natural limitations of multi-processor computer architecture. I will present work along these lines done in my group. In particular, I will focus on a new approach to calculating the free energies (stability) of different states and to overcoming "the curse of rare events". I will also discuss algorithmic improvements to multiple time step methods and to the treatment of slowly decaying, log-ranged, electrostatic effects.

Pohorille, Andrew↗
NASA NTRS2003

Job Superscheduler Architecture and Performance in Computational Grid Environments

Computational grids hold great promise in utilizing geographically separated heterogeneous resources to solve large-scale complex scientific problems. However, a number of major technical hurdles, including distributed resource management and effective job scheduling, stand in the way of realizing these gains. In this paper, we propose a novel grid superscheduler architecture and three distributed job migration algorithms. We also model the critical interaction between the superscheduler and autonomous local schedulers. Extensive performance comparisons with ideal, central, and local schemes using real workloads from leading computational centers are conducted in a simulation environment. Additionally, synthetic workloads are used to perform a detailed sensitivity analysis of our superscheduler. Several key metrics demonstrate that substantial performance gains can be achieved via smart superscheduling in distributed computational grids.

Shan, Hongzhang↗
NASA NTRS2017

Flexible Proteins at the Origin of Life

Almost all modern proteins possess well-defined, relatively rigid scaffolds that provide structural preorganization for desired functions. Such scaffolds require the sufficient length of a polypeptide chain and extensive evolutionary optimization. How ancestral proteins attained functionality, even though they were most likely markedly smaller than their contemporary descendants, remains a major, unresolved question in the origin of life. On the basis of evidence from experiments and computer simulations, we argue that at least some of the earliest water-soluble and membrane proteins were markedly more flexible than their modern counterparts. As an example, we consider a small, evolved in vitro ligase, based on a novel architecture that may be the archetype of primordial enzymes. The protein does not contain a hydrophobic core or conventional elements of the secondary structure characteristic of modern water-soluble proteins, but instead is built of a flexible, catalytic loop supported by a small hydrophilic core containing zinc atoms. It appears that disorder in the polypeptide chain imparts robustness to mutations in the protein core. Simple ion channels, likely the earliest membrane protein assemblies, could also be quite flexible, but still retain their functionality, again in contrast to their modern descendants. This is demonstrated in the example of antiamoebin, which can serve as a useful model of small peptides forming ancestral ion channels. Common features of the earliest, functional protein architectures discussed here include not only their flexibility, but also a low level of evolutionary optimization and heterogeneity in amino acid composition and, possibly, the type of peptide bonds in the protein backbone.

Flexible protein↗
NASA NTRS1995

Towards Distributed Fluids/Controls Simulations

Computational prototyping of aircraft in nonlinear regimes will require the coupling of high-order disciplines on high performance computers. This effort investigates the coupling of the Reynolds-averaged Navier-Stokes equations with six degree-of-freedom nonlinear body dynamics and controls on distributed architectures. Towards this goal, solutions obtained on a wide-node IBM SP-2, an Ethernet-linked cluster of workstations, and a Cray C90 are compared in terms of accuracy and throughput.

Atwood, Christopher A.↗
NASA NTRS1990

'Backscratching' alternative to PRSI pattern recognition

The Backscratching optical correlation algorithm has been proposed for four degree of freedom tracking. In an alternating Cartesian and log-polar implementation, the tracked parameters are scale, rotation, and two-dimenisonal translation. The algorithm has a finite capture radius in the four-dimensional tracking space. The capture radius is dependent on the tracked object, the correlator architecture, and the method of filter computation. Some methods of extending the capture radius are discussed. One is a modification of matched filters, another is a careful consideration of log-polar transform center, and another is an operational method. Some simulations of the filter construction method, in which a larger capture radius is gained at the expense of precision in determining the four parameters are presented.

Monroe, Stanley E., Jr.↗
NASA NTRS1991

Precision pointing control for an orbital earth observing system

The design concept developed for the pointing system of the high-resolution imaging spectrometer (HIRIS) which will be flown on one of NASA's earth observing system platforms is presented. The instrument is an F/5.4-aperture spectrometer with a focal length of 1222 mm, and it uses a precision two-axis gimballed mirror pointing system to image and track targets. Pointing accuracy of better than 585 arcsec (peak-to-peak), and pointing jitter of less than 2.65 arcsec in 33 ms are ensured through the use of gimbal position and basebody rate sensors. A state-space controller implemented with a digital computer is used to provide a position loop bandwidth of 1 Hz and a rate loop bandwidth of 7 Hz. An overview of the system design and flight hardware is given, the development of the controller architecture is addressed, and a simulation assessment of the pointing system that takes into consideration issues such as nonlinear effects, sensor noise, and noncollocated sensors and actuators in a flexible structure is discussed.

Robeck, Linda S.↗
NASA NTRS1991

ATAMM analysis tool

Diagnostics software for analyzing Algorithm to Architecture Mapping Model (ATAMM) based concurrent processing systems is presented. ATAMM is capable of modeling the execution of large grain algorithms on distributed data flow architectures. The tool graphically displays algorithm activities and processor activities for evaluation of the behavior and performance of an ATAMM based system. The tool's measurement capabilities indicate computing speed, throughput, concurrency, resource utilization, and overhead. Evaluations are performed on a simulated system using the software tool. The tool is used to estimate theoretical lower bound performance. Analysis results are shown to be comparable to the predictions.

Jones, Robert↗
NASA NTRS1992

Content addressable memory project

A parameterized version of the tree processor was designed and tested (by simulation). The leaf processor design is 90 percent complete. We expect to complete and test a combination of tree and leaf cell designs in the next period. Work is proceeding on algorithms for the computer aided manufacturing (CAM), and once the design is complete we will begin simulating algorithms for large problems. The following topics are covered: (1) the practical implementation of content addressable memory; (2) design of a LEAF cell for the Rutgers CAM architecture; (3) a circuit design tool user's manual; and (4) design and analysis of efficient hierarchical interconnection networks.

Hall, J. Storrs↗
NASA NTRS1990

Spaceborne autonomous multiprocessor systems

The goal of this task is to provide technology for the specification and integration of advanced processors into the Space Station Freedom data management system environment through computer performance measurement tools, simulators, and an extended testbed facility. The approach focuses on five categories: (1) user requirements--determine the suitability of existing computer technologies and systems for real-time requirements of NASA missions; (2) system performance analysis--characterize the effects of languages, architectures, and commercially available hardware on real-time benchmarks; (3) system architecture--expand NASA's capability to solve problems with integrated numeric and symbolic requirements using advanced multiprocessor architectures; (4) parallel Ada technology--extend Ada software technology to utilize parallel architectures more efficiently; and (5) testbed--extend in-house testbed to support system performance and system analysis studies.

Fernquist, Alan↗
NASA NTRS1997

Using APEX to Model Anticipated Human Error: Analysis of a GPS Navigational Aid

The interface development process can be dramatically improved by predicting design facilitated human error at an early stage in the design process. The approach we advocate is to SIMULATE the behavior of a human agent carrying out tasks with a well-specified user interface, ANALYZE the simulation for instances of human error, and then REFINE the interface or protocol to minimize predicted error. This approach, incorporated into the APEX modeling architecture, differs from past approaches to human simulation in Its emphasis on error rather than e.g. learning rate or speed of response. The APEX model consists of two major components: (1) a powerful action selection component capable of simulating behavior in complex, multiple-task environments; and (2) a resource architecture which constrains cognitive, perceptual, and motor capabilities to within empirically demonstrated limits. The model mimics human errors arising from interactions between limited human resources and elements of the computer interface whose design falls to anticipate those limits. We analyze the design of a hand-held Global Positioning System (GPS) device used for radical and navigational decisions in small yacht recalls. The analysis demonstrates how human system modeling can be an effective design aid, helping to accelerate the process of refining a product (or procedure).

VanSelst, Mark↗
NASA NTRS2003

Computation of Engine Noise Propagation and Scattering Off an Aircraft

The paper presents a comparison of experimental noise data measured in flight on a two-engine business jet aircraft with Kulite microphones placed on the suction surface of the wing with computational results. Both a time-domain discontinuous Galerkin spectral method and a frequency-domain spectral element method are used to simulate the radiation of the dominant spinning mode from the engine and its reflection and scattering by the fuselage and the wing. Both methods are implemented in computer codes that use the distributed memory model to make use of large parallel architectures. The results show that trends of the noise field are well predicted by both methods.

Xu, J.↗
NASA NTRS2012

Modeling the Flow of Rarefied Gases at NASA

At modest temperatures, the thermal energy of atmospheric diatomic gases such as nitrogen is primarily distributed between only translational and rotational energy modes. Furthermore, these energy modes are fully excited such that the specific heat at constant volume is well approximated by the simple expression C(sub v) = 5/2 R. As a result, classical mechanics provides a suitable approximation at such temperatures of the true quantum mechanical behavior of the inter-molecular collisions of such molecules. Using classical mechanics, the transfer of energy between rotational and translation energy modes is studied. The approach of Lordi and Mates is adopted to compute the trajectories and time dependent rotational orientations and energies during the collision of two non-polar diatomic molecules. A Monte-Carlo analysis is performed collecting data from the results of many such simulations in order to estimate the rotational relaxation time. A Graphical Processing Unit (GPU) is employed to improve the performance of the Monte-Carlo analysis. A comparison of the performance of the GPU implementation to an implementation on traditional computer architecture is made. Effects of the assumed inter-molecular potential on the relaxation time are studied. The seminar will also present highlights of computational analyses performed at NASA Johnson Space Center of heat transfer in rarefied gases.

Forrest E. Lumpkin, III↗
NASA NTRS2018

A Versatile Simulation Framework for Elastodynamic Modeling of Structural Health Monitoring

Structural health monitoring (SHM) has the capacity to reduce failure by detecting damage during service life, by periodic, automated monitoring. Guided Wave (GW) Ultrasound is a common SHM approach for aerospace structures. Modelling the physics of GW SHM systems provides a route for understanding system dependencies, capabilities and limitations as damage evolves during service life. Such a toolset can strengthen the understanding of the connection between GW SHM results and the true material state. The most useful modelling tools are those that provide versatile solutions with respect to the simulated component geometry and computational grid connectivity. This work details a versatile application programming interface (API) for the elastodynamic finite integration technique for modelling GW SHM of metals. The custom code implementation, EFIT-CompCell, allows for the modelling of diverse geometries by automatically balancing the message passing interface parallelization layout. The user provides the basic parameters of the simulation and the software automatically performs an initial balancing based on anticipated computational loads, and establishes the CPU communication patterns for any geometry. This work describes the programming philosophy and code structure used to create EFIT-CompCell and compares its performance and capacity to simulation tools that are more specialized for specific architectures. Results are presented for a simulation of GW SHM of an aluminum fuselage section being tested by the FAA. The simulation consists of 733M voxels which took approximately 70 hours to complete 25000 time steps using 40 Intel Xeon E5-4650v2 Ivy Bridge processor cores.

Gregory, Elizabeth D.↗
NASA NTRS2006

Computer Aided Design of Ka-Band Waveguide Power Combining Architectures for Interplanetary Spacecraft

Communication systems for future NASA interplanetary spacecraft require transmitter power ranging from several hundred watts to kilowatts. Several hybrid junctions are considered as elements within a corporate combining architecture for high power Ka-band space traveling-wave tube amplifiers (TWTAs). This report presents the simulated transmission characteristics of several hybrid junctions designed for a low loss, high power waveguide based power combiner.

Vaden, Karl R.↗
NASA NTRS2002

Software Engineering Support of the Third Round of Scientific Grand Challenge Investigations: Earth System Modeling Software Framework Survey

One of the most significant challenges in large-scale climate modeling, as well as in high-performance computing in other scientific fields, is that of effectively integrating many software models from multiple contributors. A software framework facilitates the integration task, both in the development and runtime stages of the simulation. Effective software frameworks reduce the programming burden for the investigators, freeing them to focus more on the science and less on the parallel communication implementation. while maintaining high performance across numerous supercomputer and workstation architectures. This document surveys numerous software frameworks for potential use in Earth science modeling. Several frameworks are evaluated in depth, including Parallel Object-Oriented Methods and Applications (POOMA), Cactus (from (he relativistic physics community), Overture, Goddard Earth Modeling System (GEMS), the National Center for Atmospheric Research Flux Coupler, and UCLA/UCB Distributed Data Broker (DDB). Frameworks evaluated in less detail include ROOT, Parallel Application Workspace (PAWS), and Advanced Large-Scale Integrated Computational Environment (ALICE). A host of other frameworks and related tools are referenced in this context. The frameworks are evaluated individually and also compared with each other.

Talbot, Bryan↗
NASA NTRS1994

High performance real-time flight simulation at NASA Langley

In order to meet the stringent time-critical requirements for real-time man-in-the-loop flight simulation, computer processing operations must be deterministic and be completed in as short a time as possible. This includes simulation mathematical model computational and data input/output to the simulators. In 1986, in response to increased demands for flight simulation performance, personnel at NASA's Langley Research Center (LaRC), working with the contractor, developed extensions to a standard input/output system to provide for high bandwidth, low latency data acquisition and distribution. The Computer Automated Measurement and Control technology (IEEE standard 595) was extended to meet the performance requirements for real-time simulation. This technology extension increased the effective bandwidth by a factor of ten and increased the performance of modules necessary for simulator communications. This technology is being used by more than 80 leading technological developers in the United States, Canada, and Europe. Included among the commercial applications of this technology are nuclear process control, power grid analysis, process monitoring, real-time simulation, and radar data acquisition. Personnel at LaRC have completed the development of the use of supercomputers for simulation mathematical model computational to support real-time flight simulation. This includes the development of a real-time operating system and the development of specialized software and hardware for the CAMAC simulator network. This work, coupled with the use of an open systems software architecture, has advanced the state of the art in real time flight simulation. The data acquisition technology innovation and experience with recent developments in this technology are described.

Cleveland, Jeff I., II↗
NASA NTRS1997

Rocket Engine Numerical Simulator (RENS)

Work is being done at three universities to help today's NASA engineers use the knowledge and experience of their Apolloera predecessors in designing liquid rocket engines. Ground-breaking work is being done in important subject areas to create a prototype of the most important functions for the Rocket Engine Numerical Simulator (RENS). The goal of RENS is to develop an interactive, realtime application that engineers can utilize for comprehensive preliminary propulsion system design functions. RENS will employ computer science and artificial intelligence research in knowledge acquisition, computer code parallelization and objectification, expert system architecture design, and object-oriented programming. In 1995, a 3year grant from the NASA Lewis Research Center was awarded to Dr. Douglas Moreman and Dr. John Dyer of Southern University at Baton Rouge, Louisiana, to begin acquiring knowledge in liquid rocket propulsion systems. Resources of the University of West Florida in Pensacola were enlisted to begin the process of enlisting knowledge from senior NASA engineers who are recognized experts in liquid rocket engine propulsion systems. Dr. John Coffey of the University of West Florida is utilizing his expertise in interviewing and concept mapping techniques to encode, classify, and integrate information obtained through personal interviews. The expertise extracted from the NASA engineers has been put into concept maps with supporting textual, audio, graphic, and video material. A fundamental concept map was delivered by the end of the first year of work and the development of maps containing increasing amounts of information is continuing. Find out more information about this work at the Southern University/University of West Florida. In 1996, the Southern University/University of West Florida team conducted a 4day group interview with a panel of five experts to discuss failures of the RL10 rocket engine in conjunction with the Centaur launch vehicle. The discussion was recorded on video and audio tape. Transcriptions of the entire proceedings and an abbreviated video presentation of the discussion highlights are under development. Also in 1996, two additional 3year grants were awarded to conduct parallel efforts that would complement the work being done by Southern University and the University of West Florida. Dr. Prem Bhalla of Jackson State University in Jackson, Mississippi, is developing the architectural framework for RENS. By employing the Rose Rational language and Booch Object Oriented Programming (OOP) technology, Dr. Bhalla is developing the basic structure of RENS by identifying and encoding propulsion system components, their individual characteristics, and cross-functionality and dependencies. Dr. Ruknet Cezzar of Hampton University, located in Hampton, Virginia, began working on the parallelization and objectification of rocket engine analysis and design codes. Dr. Cezzar will use the Turbo C++ OOP language to translate important liquid rocket engine computer codes from FORTRAN and permit their inclusion into the RENS framework being developed at Jackson State University. The Southern University/University of West Florida grant was extended by 1 year to coordinate the conclusion of all three efforts in 1999.

Davidian, Kenneth O.↗
NASA NTRS1979

Interpretive computer simulator for the NASA Standard Spacecraft Computer-2 (NSSC-2)

An Interpretive Computer Simulator (ICS) for the NASA Standard Spacecraft Computer-II (NSSC-II) was developed as a code verification and testing tool for the Annular Suspension and Pointing System (ASPS) project. The simulator is written in the higher level language PASCAL and implented on the CDC CYBER series computer system. It is supported by a metal assembler, a linkage loader for the NSSC-II, and a utility library to meet the application requirements. The architectural design of the NSSC-II is that of an IBM System/360 (S/360) and supports all but four instructions of the S/360 standard instruction set. The structural design of the ICS is described with emphasis on the design differences between it and the NSSC-II hardware. The program flow is diagrammed, with the function of each procedure being defined; the instruction implementation is discussed in broad terms; and the instruction timings used in the ICS are listed. An example of the steps required to process an assembly level language program on the ICS is included. The example illustrates the control cards necessary to assemble, load, and execute assembly language code; the sample program to to be executed; the executable load module produced by the loader; and the resulting output produced by the ICS.

Smith, R. S.↗