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NASA NTRS2005

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

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

Yoon, Seokkwan↗
NASA NTRS2005

Life in the fast lane for protein crystallization and X-ray crystallography

The common goal for structural genomic centers and consortiums is to decipher as quickly as possible the three-dimensional structures for a multitude of recombinant proteins derived from known genomic sequences. Since X-ray crystallography is the foremost method to acquire atomic resolution for macromolecules, the limiting step is obtaining protein crystals that can be useful of structure determination. High-throughput methods have been developed in recent years to clone, express, purify, crystallize and determine the three-dimensional structure of a protein gene product rapidly using automated devices, commercialized kits and consolidated protocols. However, the average number of protein structures obtained for most structural genomic groups has been very low compared to the total number of proteins purified. As more entire genomic sequences are obtained for different organisms from the three kingdoms of life, only the proteins that can be crystallized and whose structures can be obtained easily are studied. Consequently, an astonishing number of genomic proteins remain unexamined. In the era of high-throughput processes, traditional methods in molecular biology, protein chemistry and crystallization are eclipsed by automation and pipeline practices. The necessity for high-rate production of protein crystals and structures has prevented the usage of more intellectual strategies and creative approaches in experimental executions. Fundamental principles and personal experiences in protein chemistry and crystallization are minimally exploited only to obtain "low-hanging fruit" protein structures. We review the practical aspects of today's high-throughput manipulations and discuss the challenges in fast pace protein crystallization and tools for crystallography. Structural genomic pipelines can be improved with information gained from low-throughput tactics that may help us reach the higher-bearing fruits. Examples of recent developments in this area are reported from the efforts of the Southeast Collaboratory for Structural Genomics (SECSG).

Review↗
NASA NTRS2005

Photo-realistic Terrain Modeling and Visualization for Mars Exploration Rover Science Operations

Modern NASA planetary exploration missions employ complex systems of hardware and software managed by large teams of. engineers and scientists in order to study remote environments. The most complex and successful of these recent projects is the Mars Exploration Rover mission. The Computational Sciences Division at NASA Ames Research Center delivered a 30 visualization program, Viz, to the MER mission that provides an immersive, interactive environment for science analysis of the remote planetary surface. In addition, Ames provided the Athena Science Team with high-quality terrain reconstructions generated with the Ames Stereo-pipeline. The on-site support team for these software systems responded to unanticipated opportunities to generate 30 terrain models during the primary MER mission. This paper describes Viz, the Stereo-pipeline, and the experiences of the on-site team supporting the scientists at JPL during the primary MER mission.

Edwards, Laurence↗
NASA NTRS1977

Heat Pipes For Alyeska

The heat pipes job is to keep the arctic ground frozen. The permafrost soil alternately freezes and thaws with seasonal temperature changes causing surface dislocations and problems for the builders. In winter, a phenomenon called frost-heaving uplifts the soil. It is something like the creation of highway potholes by the freezing of rainwater below the roadbed, but frost-heaving exerts a far greater force. Thawing of the frost in the summer causes the soil to settle unevenly. Therefore it is necessary to keep the soil in a continually frozen state so the pipeline won't rupture. To solve this problem, McDonnell Douglas Corp. applied heat pipe principles in the design of the vertical supports that hold up the pipeline.

Source record↗
NASA NTRS2004

New Software for Ensemble Creation in the Spitzer-Space-Telescope Operations Database

Some of the computer pipelines used to process digital astronomical images from NASA's Spitzer Space Telescope require multiple input images, in order to generate high-level science and calibration products. The images are grouped into ensembles according to well documented ensemble-creation rules by making explicit associations in the operations Informix database at the Spitzer Science Center (SSC). The advantage of this approach is that a simple database query can retrieve the required ensemble of pipeline input images. New and improved software for ensemble creation has been developed. The new software is much faster than the existing software because it uses pre-compiled database stored-procedures written in Informix SPL (SQL programming language). The new software is also more flexible because the ensemble creation rules are now stored in and read from newly defined database tables. This table-driven approach was implemented so that ensemble rules can be inserted, updated, or deleted without modifying software.

Spitzer Science Center (SSC)↗
NASA NTRS2008

GSFC Technical Outreach: The Capitol College Model

In February 2005, as part of the National Aeronautic and Space Administration (NASA) Technical Outreach Program, Goddard Space Flight Center (GSFC) awarded Capitol College of Laurel, Maryland an Educational Grant to establish a Space Operation academic curriculum to meet the future needs of mission operations engineers. This was in part due to the aerospace industry and GSFC concerns that a large number of professional engineers are projected to retire in the near term with evidence showing that current enrollment in engineering schools will not produce sufficient number of space operation trained engineers that will meet industry and government demands. Capitol College, under the agreement of the Educational Grant, established the Space Operations Institute (SOI) with a new curriculum in Space Operations that was approved and certified by the State of Maryland. The SO1 programs focuses on attracting, recruiting, and training a pipeline of highly qualified engineers with experience in mission operations, system engineering and development. The selected students are integrated as members of the engineering support team in any of the missions supported by the institute. The students are mentored by professional engineers from several aerospace companies that support GSFC. Initially, the institute was involved in providing console engineers and mission planning trainees for the Upper Atmosphere Research Satellite (UARS), the Earth Radiation Budget Satellite (ERBS) and the Total Ozone Mapping Spectrometer mission (TOMS). Subsequently, the students were also involved in the technology refresh of the TOMS ground system and other mission operations development. Further mission assignment by GSFC management included participation in the Tropical Rainfall Measuring Mission (TRMM) mission operations and ground system technology refresh. The SOI program has been very successful. Since October 2005, sixty-four students have been enrolled in the SOI program and twenty-five have already graduated from the program, nineteen of whom are employed by company's supporting GSFC. Due to the success of the program, the initial grant period was extended for another period of two years. This paper presents the process that established the SOI as a viable pipeline of mission operations engineers, the lessons learned in the process of dealing with grants, and experience gained in mentoring engineering students that are responsible for particular areas of expertise and functionality. This paper can also be considered a case study and model for integrating a student team with government and industry professionals in the real world of mission operations.

Marius, Julio L.↗
NASA NTRS2009

Hardware Implementation of a Bilateral Subtraction Filter

A bilateral subtraction filter has been implemented as a hardware module in the form of a field-programmable gate array (FPGA). In general, a bilateral subtraction filter is a key subsystem of a high-quality stereoscopic machine vision system that utilizes images that are large and/or dense. Bilateral subtraction filters have been implemented in software on general-purpose computers, but the processing speeds attainable in this way even on computers containing the fastest processors are insufficient for real-time applications. The present FPGA bilateral subtraction filter is intended to accelerate processing to real-time speed and to be a prototype of a link in a stereoscopic-machine- vision processing chain, now under development, that would process large and/or dense images in real time and would be implemented in an FPGA. In terms that are necessarily oversimplified for the sake of brevity, a bilateral subtraction filter is a smoothing, edge-preserving filter for suppressing low-frequency noise. The filter operation amounts to replacing the value for each pixel with a weighted average of the values of that pixel and the neighboring pixels in a predefined neighborhood or window (e.g., a 9 9 window). The filter weights depend partly on pixel values and partly on the window size. The present FPGA implementation of a bilateral subtraction filter utilizes a 9 9 window. This implementation was designed to take advantage of the ability to do many of the component computations in parallel pipelines to enable processing of image data at the rate at which they are generated. The filter can be considered to be divided into the following parts (see figure): a) An image pixel pipeline with a 9 9- pixel window generator, b) An array of processing elements; c) An adder tree; d) A smoothing-and-delaying unit; and e) A subtraction unit. After each 9 9 window is created, the affected pixel data are fed to the processing elements. Each processing element is fed the pixel value for its position in the window as well as the pixel value for the central pixel of the window. The absolute difference between these two pixel values is calculated and used as an address in a lookup table. Each processing element has a lookup table, unique for its position in the window, containing the weight coefficients for the Gaussian function for that position. The pixel value is multiplied by the weight, and the outputs of the processing element are the weight and pixel-value weight product. The products and weights are fed to the adder tree. The sum of the products and the sum of the weights are fed to the divider, which computes the sum of products the sum of weights. The output of the divider is denoted the bilateral smoothed image. The smoothing function is a simple weighted average computed over a 3 3 subwindow centered in the 9 9 window. After smoothing, the image is delayed by an additional amount of time needed to match the processing time for computing the bilateral smoothed image. The bilateral smoothed image is then subtracted from the 3 3 smoothed image to produce the final output. The prototype filter as implemented in a commercially available FPGA processes one pixel per clock cycle. Operation at a clock speed of 66 MHz has been demonstrated, and results of a static timing analysis have been interpreted as suggesting that the clock speed could be increased to as much as 100 MHz.

Huertas, Andres↗
NASA NTRS2010

Kepler Data Release 3 Notes

This describes the collection of data and the processing done on it so when researchers around the world get the Kepler data sets (which are a set of pixels from the telescope of a particular target (star, galaxy or whatever) over a 3 month period) they can adjust their algorithms fro things that were done (like subtracting all of one particular wavelength for example). This is used to calibrate their own algorithms so that they know what it is they are starting with. It is posted so that whoever is accessing the publicly available data (not all of it is made public) can understand it .. (most of the Kepler data is under restriction for 1 - 4 years and is not available, but the handbook is for everyone (public and restricted) The Data Analysis Working Group have released long and short cadence materials, including FFls and Dropped Targets for the Public. The Kepler Science Office considers Data Release 3 to provide "browse quality" data. These notes have been prepared to give Kepler users of the Multimission Archive at STScl (MAST) a summary of how the data were collected and prepared, and how well the data processing pipeline is functioning on flight data. They will be updated for each release of data to the public archive and placed on MAST along with other Kepler documentation, at http:// archive.stsci.edu/kepler/documents.html .Data release 3 is meant to give users the opportunity to examine the data for possibly interesting science and to involve the users in improving the pipeline for future data releases. To perform the latter service, users are encouraged to notice and document artifacts, either in the raw or processed data, and report them to the Science Office.

Cleve, Jeffrey E.↗
NASA NTRS2010

Kepler Data Release 4 Notes

The Data Analysis Working Group have released long and short cadence materials, including FFIs and Dropped Targets for the Public. The Kepler Science Office considers Data Release 4 to provide "browse quality" data. These notes have been prepared to give Kepler users of the Multimission Archive at STScl (MAST) a summary of how the data were collected and prepared, and how well the data processing pipeline is functioning on flight data. They will be updated for each release of data to the public archive and placed on MAST along with other Kepler documentation, at http://archive.stsci.edu/kepler/documents.html. Data release 3 is meant to give users the opportunity to examine the data for possibly interesting science and to involve the users in improving the pipeline for future data releases. To perform the latter service, users are encouraged to notice and document artifacts, either in the raw or processed data, and report them to the Science Office.

Van Cleve, Jeffrey↗
NASA NTRS2010

Rapid Corner Detection Using FPGAs

In order to perform precision landings for space missions, a control system must be accurate to within ten meters. Feature detection applied against images taken during descent and correlated against the provided base image is computationally expensive and requires tens of seconds of processing time to do just one image while the goal is to process multiple images per second. To solve this problem, this algorithm takes that processing load from the central processing unit (CPU) and gives it to a reconfigurable field programmable gate array (FPGA), which is able to compute data in parallel at very high clock speeds. The workload of the processor then becomes simpler; to read an image from a camera, it is transferred into the FPGA, and the results are read back from the FPGA. The Harris Corner Detector uses the determinant and trace to find a corner score, with each step of the computation occurring on independent clock cycles. Essentially, the image is converted into an x and y derivative map. Once three lines of pixel information have been queued up, valid pixel derivatives are clocked into the product and averaging phase of the pipeline. Each x and y derivative is squared against itself, as well as the product of the ix and iy derivative, and each value is stored in a WxN size buffer, where W represents the size of the integration window and N is the width of the image. In this particular case, a window size of 5 was chosen, and the image is 640 480. Over a WxN size window, an equidistance Gaussian is applied (to bring out the stronger corners), and then each value in the entire window is summed and stored. The required components of the equation are in place, and it is just a matter of taking the determinant and trace. It should be noted that the trace is being weighted by a constant k, a value that is found empirically to be within 0.04 to 0.15 (and in this implementation is 0.05). The constant k determines the number of corners available to be compared against a threshold sigma to mark a valid corner. After a fixed delay from when the first pixel is clocked in (to fill the pipeline), a score is achieved after each successive clock. This score corresponds with an (x,y) location within the image. If the score is higher than the predetermined threshold sigma, then a flag is set high and the location is recorded.

Morfopoulos, Arin C.↗
NASA NTRS2007

NavP: Structured and Multithreaded Distributed Parallel Programming

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

navigational programming (NavP)↗
NASA NTRS2011

Framework for Integrating Science Data Processing Algorithms Into Process Control Systems

A software framework called PCS Task Wrapper is responsible for standardizing the setup, process initiation, execution, and file management tasks surrounding the execution of science data algorithms, which are referred to by NASA as Product Generation Executives (PGEs). PGEs codify a scientific algorithm, some step in the overall scientific process involved in a mission science workflow. The PCS Task Wrapper provides a stable operating environment to the underlying PGE during its execution lifecycle. If the PGE requires a file, or metadata regarding the file, the PCS Task Wrapper is responsible for delivering that information to the PGE in a manner that meets its requirements. If the PGE requires knowledge of upstream or downstream PGEs in a sequence of executions, that information is also made available. Finally, if information regarding disk space, or node information such as CPU availability, etc., is required, the PCS Task Wrapper provides this information to the underlying PGE. After this information is collected, the PGE is executed, and its output Product file and Metadata generation is managed via the PCS Task Wrapper framework. The innovation is responsible for marshalling output Products and Metadata back to a PCS File Management component for use in downstream data processing and pedigree. In support of this, the PCS Task Wrapper leverages the PCS Crawler Framework to ingest (during pipeline processing) the output Product files and Metadata produced by the PGE. The architectural components of the PCS Task Wrapper framework include PGE Task Instance, PGE Config File Builder, Config File Property Adder, Science PGE Config File Writer, and PCS Met file Writer. This innovative framework is really the unifying bridge between the execution of a step in the overall processing pipeline, and the available PCS component services as well as the information that they collectively manage.

Mattmann, Chris A.↗
NASA NTRS2011

Dynamic Black-Level Correction and Artifact Flagging for Kepler Pixel Time Series

Methods applied to the calibration stage of Kepler pipeline data processing [1] (CAL) do not currently use all of the information available to identify and correct several instrument-induced artifacts. These include time-varying crosstalk from the fine guidance sensor (FGS) clock signals, and manifestations of drifting moire pattern as locally correlated nonstationary noise, and rolling bands in the images which find their way into the time series [2], [3]. As the Kepler Mission continues to improve the fidelity of its science data products, we are evaluating the benefits of adding pipeline steps to more completely model and dynamically correct the FGS crosstalk, then use the residuals from these model fits to detect and flag spatial regions and time intervals of strong time-varying black-level which may complicate later processing or lead to misinterpretation of instrument behavior as stellar activity.

Kolodziejczak, J. J.↗
NASA NTRS2012

Parametric Deformation of Discrete Geometry for Aerodynamic Shape Design

We present a versatile discrete geometry manipulation platform for aerospace vehicle shape optimization. The platform is based on the geometry kernel of an open-source modeling tool called Blender and offers access to four parametric deformation techniques: lattice, cage-based, skeletal, and direct manipulation. Custom deformation methods are implemented as plugins, and the kernel is controlled through a scripting interface. Surface sensitivities are provided to support gradient-based optimization. The platform architecture allows the use of geometry pipelines, where multiple modelers are used in sequence, enabling manipulation difficult or impossible to achieve with a constructive modeler or deformer alone. We implement an intuitive custom deformation method in which a set of surface points serve as the design variables and user-specified constraints are intrinsically satisfied. We test our geometry platform on several design examples using an aerodynamic design framework based on Cartesian grids. We examine inverse airfoil design and shape matching and perform lift-constrained drag minimization on an airfoil with thickness constraints. A transport wing-fuselage integration problem demonstrates the approach in 3D. In a final example, our platform is pipelined with a constructive modeler to parabolically sweep a wingtip while applying a 1-G loading deformation across the wingspan. This work is an important first step towards the larger goal of leveraging the investment of the graphics industry to improve the state-of-the-art in aerospace geometry tools.

Anderson, George R.↗
NASA NTRS2012

3D Visualization for Phoenix Mars Lander Science Operations

Planetary surface exploration missions present considerable operational challenges in the form of substantial communication delays, limited communication windows, and limited communication bandwidth. A 3D visualization software was developed and delivered to the 2008 Phoenix Mars Lander (PML) mission. The components of the system include an interactive 3D visualization environment called Mercator, terrain reconstruction software called the Ames Stereo Pipeline, and a server providing distributed access to terrain models. The software was successfully utilized during the mission for science analysis, site understanding, and science operations activity planning. A terrain server was implemented that provided distribution of terrain models from a central repository to clients running the Mercator software. The Ames Stereo Pipeline generates accurate, high-resolution, texture-mapped, 3D terrain models from stereo image pairs. These terrain models can then be visualized within the Mercator environment. The central cross-cutting goal for these tools is to provide an easy-to-use, high-quality, full-featured visualization environment that enhances the mission science team s ability to develop low-risk productive science activity plans. In addition, for the Mercator and Viz visualization environments, extensibility and adaptability to different missions and application areas are key design goals.

Edwards, Laurence↗
NASA NTRS2012

Implementation and Testing of the First Prompt Search for Electromagnetic Counterparts to Gravitational Wave Transients

A transient astrophysical event observed in both gravitational wave (OW) and electromagnetic (EM) channels would yield rich scientific rewards. A first program initiating EM follow-ups to possible transient OW events has been developed and exercised by the LIGO and Virgo community in association with several partners. In this paper, we describe and evaluate the methods used to promptly identify and localize OW event candidates and to request images of targeted sky locations. Methods. During two observing periods (Dec 172009 to Jan 8 2010 and Sep 2 to Oct 20 2010), a low-latency analysis pipeline was used to identify OW event candidates and to reconstruct maps of possible sky locations. A catalog of nearby galaxies and Milky Way globular clusters was used to select the most promising sky positions to be imaged, and this directional information was delivered to EM observatories with time lags of about thirty minutes. A Monte Carlo simulation has been used to evaluate the low-latency OW pipeline's ability to reconstruct source positions correctly. Results. For signals near the detection threshold, our low-latency algorithms often localized simulated GW burst signals to tens of square degrees, while neutron star/neutron star inspirals and neutron star/black hole inspirals were localized to a few hundred square degrees. Localization precision improves for moderately stronger signals. The correct sky location of signals well above threshold and originating from nearby galaxies may be observed with approx.50% or better probability with a few pointings of wide-field telescopes. Key words. gravitational waves - methods: observational

Camp, Jordan↗
NASA NTRS2011

Implementation and Testing of the First Prompt for Electromagnetic Counterparts to Gravitational Wave Transients

A transient astrophysical event observed in both gravitational wave (GW) and electromagnetic (EM) channels would yield rich scientific rewards. A first program initiating EM follow-ups to possible transient GW events has been developed and exercised by the LIGO and Virgo community in association with several partners. In this paper, we describe and evaluate the methods used to promptly identify and localize GW event candidates and to request images of targeted sky locations. Methods. During two observing periods (Dec 17 2009 to Jan 8 2010 and Sep 2 to Oct 20 2010), a low-latency analysis pipeline was used to identify GW-event candidates and to reconstruct-maps of possible sky locations. A catalog of nearby galaxies and Milky Way globular clusters was used to select the most promising sky positions to be imaged, and this directional information was delivered to EM observatories with time lags of about thirty minutes. A Monte Carlo simulation has been used to evaluate the low-latency GW pipeline s ability to reconstruct source positions correctly. Results. For signals near the detection threshold, our low-latency algorithms often localized simulated GW burst signals to tens of square degrees, while neutron star/neutron star inspirals and neutron star/black hole inspirals were localized to a few hundred square degrees. Localization precision improves for moderately stronger signals. The correct sky location of signals well above threshold and originating from nearby galaxies may be observed with 50% or better probability with a few pointings of wide-field telescopes.

Abadie, J.↗
NASA NTRS2011

Automated X-ray and Optical Analysis of the Virtual Observatory and Grid Computing

We are developing a system to combine the Web Enabled Source Identification with X-Matching (WESIX) web service, which emphasizes source detection on optical images,with the XAssist program that automates the analysis of X-ray data. XAssist is continuously processing archival X-ray data in several pipelines. We have established a workflow in which FITS images and/or (in the case of X ray data) an X-ray field can be input to WESIX. Intelligent services return available data (if requested fields have been processed) or submit job requests to a queue to be performed asynchronously. These services will be available via web services (for non-interactive use by Virtual Observatory portals and applications) and through web applications (written in the Django web application framework). We are adding web services for specific XAssist functionality such as determining .the exposure and limiting flux for a given position on the sky and extracting spectra and images for a given region. We are improving the queuing system in XAssist to allow for "watch lists" to be specified by users, and when X-ray fields in a user's watch list become publicly available they will be automatically added to the queue. XAssist is being expanded to be used as a survey planning 1001 when coupled with simulation software, including functionality for NuStar, eRosita, IXO, and the Wide Field Xray Telescope (WFXT), as part of an end to end simulation/analysis system. We are also investigating the possibility of a dedicated iPhone/iPad app for querying pipeline data, requesting processing, and administrative job control.

Ptak, A.↗