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NASA NTRS2001

Efficiency of parallel direct optimization

Tremendous progress has been made at the level of sequential computation in phylogenetics. However, little attention has been paid to parallel computation. Parallel computing is particularly suited to phylogenetics because of the many ways large computational problems can be broken into parts that can be analyzed concurrently. In this paper, we investigate the scaling factors and efficiency of random addition and tree refinement strategies using the direct optimization software, POY, on a small (10 slave processors) and a large (256 slave processors) cluster of networked PCs running LINUX. These algorithms were tested on several data sets composed of DNA and morphology ranging from 40 to 500 taxa. Various algorithms in POY show fundamentally different properties within and between clusters. All algorithms are efficient on the small cluster for the 40-taxon data set. On the large cluster, multibuilding exhibits excellent parallel efficiency, whereas parallel building is inefficient. These results are independent of data set size. Branch swapping in parallel shows excellent speed-up for 16 slave processors on the large cluster. However, there is no appreciable speed-up for branch swapping with the further addition of slave processors (>16). This result is independent of data set size. Ratcheting in parallel is efficient with the addition of up to 32 processors in the large cluster. This result is independent of data set size. c2001 The Willi Hennig Society.

NASA Discipline Evolutionary Biology↗

NASA NTRS2013

Analyzing Tropical Waves Using the Parallel Ensemble Empirical Model Decomposition Method: Preliminary Results from Hurricane Sandy

In this study, we discuss the performance of the parallel ensemble empirical mode decomposition (EMD) in the analysis of tropical waves that are associated with tropical cyclone (TC) formation. To efficiently analyze high-resolution, global, multiple-dimensional data sets, we first implement multilevel parallelism into the ensemble EMD (EEMD) and obtain a parallel speedup of 720 using 200 eight-core processors. We then apply the parallel EEMD (PEEMD) to extract the intrinsic mode functions (IMFs) from preselected data sets that represent (1) idealized tropical waves and (2) large-scale environmental flows associated with Hurricane Sandy (2012). Results indicate that the PEEMD is efficient and effective in revealing the major wave characteristics of the data, such as wavelengths and periods, by sifting out the dominant (wave) components. This approach has a potential for hurricane climate study by examining the statistical relationship between tropical waves and TC formation.

PEEMD↗

NASA NTRS1989

Hardware impacts to software development strategies - The history of the development of the Mars Observer Payload Data Subsystem embedded real-time software

Ways in which parallel hardware development and high level requirements changes have influenced Mars Observer Payload Data Subsystem (PDS) flight software development are discussed. Particular attention is given to ways in which the evolving hardware product and changing requirements have led to repeated modification to software requirements, design, code, and test tools and a delay in the closure of corresponding phases of the software development life cycle. Design and implementation problems which were encountered during the PDS software development effort are described.

Elson, Anne B.↗

NASA NTRS1991

System Decommutes And Displays Telemetry Data

TDPlus computer program software system for decommutation of pulse-code-modulation (PCM) telemetry signals. Provides synchronization, conversion into engineering units, and display of serial bit streams. Transforms IBM PC-compatible computer into PCM-telemetry-decommutation system. Synchronizes telemetric signals data and enables conversion back into such meaningful forms as voltage, current, pressure, and the like. Also controls operation of digital-to-analog converters to ship data to paper strip charts or to parallel digital ports for offloading to other computers. Software used to process actual data only when telemetry-data-processing computer modified in accordance with specifications contained in "TDPlus TM Data Processor" (GSC-13291). Written in Turbo C and 8088 Assembly language.

Massey, D. E.↗

NASA NTRS2001

An OFDM System Using Polyphase Filter and DFT Architecture for Very High Data Rate Applications

This paper presents a conceptual architectural design of a four-channel Orthogonal Frequency Division Multiplexing (OFDM) system with an aggregate information throughput of 622 megabits per second (Mbps). Primary emphasis is placed on the generation and detection of the composite waveform using polyphase filter and Discrete Fourier Transform (DFT) approaches to digitally stack and bandlimit the individual carriers. The four-channel approach enables the implementation of a system that can be both power and bandwidth efficient, yet enough parallelism exists to meet higher data rate goals. It also enables a DC power efficient transmitter that is suitable for on-board satellite systems, and a moderately complex receiver that is suitable for low-cost ground terminals. The major advantage of the system as compared to a single channel system is lower complexity and DC power consumption. This is because the highest sample rate is half that of the single channel system and synchronization can occur at most, depending on the synchronization technique, a quarter of the rate of a single channel system. The major disadvantage is the increased peak-to-average power ratio over the single channel system. Simulation results in a form of bit-error-rate (BER) curves are presented in this paper.

Kifle, Muli↗

NASA NTRS1997

High Performance Morphological Filtering of Cirrus Emission from Infrared Images

The project was designed to explore new morphological filtering, techniques for the removal of foreground Galactic 'Cirrus' emission from NASA Infrared Astronomical Satellite (IRAS) data, especially at 100 microns, using parallel processors as the main engine for achieving this result. The ultimate aim was to provide NASA with completely filtered data by the end of the grant period for the entire IRAS 100 and possibly 60 micron database. If successful, the filtered data would reveal many new sources of IR emission, especially at low galactic latitudes, which had previously been heavily confused with diffuse Galactic 'cirrus'.

Appleton, P. N.↗

NASA NTRSDate not supplied

Nanopore Sequencing-Based Microbial Air Profiling Method for Crewed Spacecraft

Microbial monitoring of the International Space Station (ISS) atmosphere is vital to maintaining the health of the spacecraft and crew. Key to NASA’s microbial risk assessment is the identity of contaminating microorganisms in the environment. Historically, this has been achieved through impaction-based air sampling followed by culture. Identification of the microorganisms present requires sample return to Earth and lab-based analyses. While this culture-based approach has served to provide alerts to anomalies and overall confidence in the controls in place, it is not suitable for exploration missions with no sample return. Recently, significant advancements in molecular-based microbial monitoring via nanopore sequencing have been implemented onboard the ISS. Building on this work, multiple commercially available air samplers, compatible with downstream molecular analysis, were evaluated for use in the spaceflight environment. Through this assessment, the Coriolis Compact (Bertin Technologies), which uses cyclonic technology to collect bioaerosols onto the surface of a sterile cone, was selected for a larger-scale comparison to the current culture-based monitoring method. Using the Coriolis Compact, 1000 L of air was collected from the breakroom of an office building and a fitness center. The buffer used to dissociate the microbial cells from the surface of the cone was split between the NASA Microbiology Laboratory’s standard culture and Sanger sequencing-based method and the culture-independent nanopore sequencing method. The bacteria identified through culture were present in the nanopore data, with Micrococcus, Staphylococcus, and Moraxella being the most common cultured isolates, which is expected based on the media and growth conditions. Not surprisingly, the nanopore data yielded much higher diversity and paralleled that of previous atmospheric microbiome studies of human-occupied built environments. As compared to the culture-based data where the breakroom and fitness center data sets cluster in proximity, the nanopore data depicts the contrast of these atmospheric microbiomes. Moreover, the nanopore data were sufficient to meet NASA’s risk assessment needs and noted the culturable isolates routinely observed. This nanopore-based atmospheric microbial profiling method will enable near real-time environmental monitoring of crewed spacecraft as future missions extend beyond low-Earth orbit.

Brandon Dunbar↗

NASA NTRS1977

Analysis of low altitude atmospheric turbulence data measured in flight

All three components of turbulence were measured simultaneously in flight at each wing tip of a Beech D-18 aircraft. The flights were conducted at low altitude, 30.5 - 61.0 meters (100-200 ft.), over water in the presence of wind driven turbulence. Statistical properties of flight measured turbulence were compared with Gaussian and non-Gaussian turbulence models. Spatial characteristics of the turbulence were analyzed using the data from flight perpendicular and parallel to the wind. The probability density distributions of the vertical gusts show distinctly non-Gaussian characteristics. The distributions of the longitudinal and lateral gusts are generally Gaussian. The power spectra compare in the inertial subrange at some points better with the Dryden spectrum, while at other points the von Karman spectrum is a better approximation. In the low frequency range the data show peaks or dips in the power spectral density. The cross between vertical gusts in the direction of the mean wind were compared with a matched non-Gaussian model. The real component of the cross spectrum is in general close to the non-Gaussian model. The imaginary component, however, indicated a larger phase shift between these two gust components than was found in previous research.

Ganzer, V. M.↗

NASA NTRS1972

Post-analysis report on Chesapeake Bay data processing

The additional processing performed on data collected over the Rhode River Test Site and Forestry Site in November 1970 is reported. The techniques and procedures used to obtain the processed results are described. Thermal data collected over three approximately parallel lines of the site were contoured, and the results color coded, for the purpose of delineating important scene constituents and to identify trees attacked by pine bark beetles. Contouring work and histogram preparation are reviewed and the important conclusions from the spectral analysis and recognition computer (SPARC) signature extension work are summarized. The SPARC setup and processing records are presented and recommendations are made for future data collection over the site.

Thomson, F.↗

NASA NTRS1997

High Performance Input/Output Systems for High Performance Computing and Four-Dimensional Data Assimilation

The approach of this task was to apply leading parallel computing research to a number of existing techniques for assimilation, and extract parameters indicating where and how input/output limits computational performance. The following was used for detailed knowledge of the application problems: 1. Developing a parallel input/output system specifically for this application 2. Extracting the important input/output characteristics of data assimilation problems; and 3. Building these characteristics s parameters into our runtime library (Fortran D/High Performance Fortran) for parallel input/output support.

Fox, Geoffrey C.↗

NASA NTRS1999

Parallelization of the Physical-Space Statistical Analysis System (PSAS)

Atmospheric data assimilation is a method of combining observations with model forecasts to produce a more accurate description of the atmosphere than the observations or forecast alone can provide. Data assimilation plays an increasingly important role in the study of climate and atmospheric chemistry. The NASA Data Assimilation Office (DAO) has developed the Goddard Earth Observing System Data Assimilation System (GEOS DAS) to create assimilated datasets. The core computational components of the GEOS DAS include the GEOS General Circulation Model (GCM) and the Physical-space Statistical Analysis System (PSAS). The need for timely validation of scientific enhancements to the data assimilation system poses computational demands that are best met by distributed parallel software. PSAS is implemented in Fortran 90 using object-based design principles. The analysis portions of the code solve two equations. The first of these is the "innovation" equation, which is solved on the unstructured observation grid using a preconditioned conjugate gradient (CG) method. The "analysis" equation is a transformation from the observation grid back to a structured grid, and is solved by a direct matrix-vector multiplication. Use of a factored-operator formulation reduces the computational complexity of both the CG solver and the matrix-vector multiplication, rendering the matrix-vector multiplications as a successive product of operators on a vector. Sparsity is introduced to these operators by partitioning the observations using an icosahedral decomposition scheme. PSAS builds a large (approx. 128MB) run-time database of parameters used in the calculation of these operators. Implementing a message passing parallel computing paradigm into an existing yet developing computational system as complex as PSAS is nontrivial. One of the technical challenges is balancing the requirements for computational reproducibility with the need for high performance. The problem of computational reproducibility is well known in the parallel computing community. It is a requirement that the parallel code perform calculations in a fashion that will yield identical results on different configurations of processing elements on the same platform. In some cases this problem can be solved by sacrificing performance. Meeting this requirement and still achieving high performance is very difficult. Topics to be discussed include: current PSAS design and parallelization strategy; reproducibility issues; load balance vs. database memory demands, possible solutions to these problems.

Larson, J. W.↗

NASA NTRS1975

Evaluation of ERTS multispectral signatures in relation to ground control signatures using a nested-sampling approach

The author has identified the following significant results. Ground measured spectral signatures of wavelength bands matching ERTS MSS were collected using a radiometer at several Californian and Nevadan sites, and directly compared with similar data from ERTS CCTs. The comparison was tested at the highest possible spatial resolution for ERTS, using deconvoluted MSS data, and contrasted with that of ground measured spectra, originally from 1 meter squares. In the mobile traverses of the grassland sites, these one meter fields of view were integrated into eighty meter transects along the five km track across four major rock/soil types. Suitable software was developed to read the MSS CCT tapes, to shadeprint individual bands with user-determined greyscale stretching. Four new algorithms for unsupervised and supervised, normalized and unnormalized clustering were developed, into a program termed STANSORT. Parallel software allowed the field data to be calibrated, and by using concurrently continuously collected, upward- and downward-viewing, 4 band radiometers, bidirectional reflectances could be calculated.

Lyon, R. J. P.↗

NASA NTRS1986

Mountain building processes in the Central Andes

False color composite images of the Thematic Mapper (TM) bands 5, 4, and 2 were examined to make visual interpretations of geological features. The use of the roam mode of image display with the International Imaging Systems (IIS) System 600 image processing package running on the IIS Model 75 was very useful. Several areas in which good comparisons with ground data existed, were examined in detail. Parallel to the visual approach, image processing methods are being developed which allow the complete use of the seven TM bands. The data was organized into easily accessible files and a visual cataloging of the quads (quarter TM scenes) with preliminary registration with the best available charts for the region. The catalog has proved to be a valuable tool for the rapid scanning of quads for a specific investigation. Integration of the data into a complete approach to the problems of uplift, deformation, and magnetism in relation to the Nazca-South American plate interaction is at an initial stage.

Bloom, A. L.↗

NASA NTRS1994

Analysis and Optimization of Parallel Software Pipeline Performance

Pipelining is a common strategy for extracting parallelism from a collection of independent computational tasks, each of which is spread among a number of processors and has an implied data dependence. When implemented on MIMD parallel computers with finite process interrupt times, pipeline algorithms suffer from slowdown--in addition to the expected pipeline fill time--due to a wave-like propagation of delays. This phenomenon, which has been observed experimentally using the performance monitoring system AIMS, is investigated analytically, and an optimal correction is derived to eliminate the wave. Efficiency increase through the correction is verified experimentally.

VanderWijngaart, Rob F.↗

NASA NTRS1995

The Effect of Interrupts on Software Pipeline Execution on Message-Passing Architectures

VanderWijngaart, Rob F.↗

NASA NTRS2017

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

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

Rose, Geoffrey K.↗

NASA NTRS1993

Efficiently modeling neural networks on massively parallel computers

Neural networks are a very useful tool for analyzing and modeling complex real world systems. Applying neural network simulations to real world problems generally involves large amounts of data and massive amounts of computation. To efficiently handle the computational requirements of large problems, we have implemented at Los Alamos a highly efficient neural network compiler for serial computers, vector computers, vector parallel computers, and fine grain SIMD computers such as the CM-2 connection machine. This paper describes the mapping used by the compiler to implement feed-forward backpropagation neural networks for a SIMD (Single Instruction Multiple Data) architecture parallel computer. Thinking Machines Corporation has benchmarked our code at 1.3 billion interconnects per second (approximately 3 gigaflops) on a 64,000 processor CM-2 connection machine (Singer 1990). This mapping is applicable to other SIMD computers and can be implemented on MIMD computers such as the CM-5 connection machine. Our mapping has virtually no communications overhead with the exception of the communications required for a global summation across the processors (which has a sub-linear runtime growth on the order of O(log(number of processors)). We can efficiently model very large neural networks which have many neurons and interconnects and our mapping can extend to arbitrarily large networks (within memory limitations) by merging the memory space of separate processors with fast adjacent processor interprocessor communications. This paper will consider the simulation of only feed forward neural network although this method is extendable to recurrent networks.

Farber, Robert M.↗

NASA NTRS1995

Spectral identification of minerals using imaging spectrometry data: Evaluating the effects of signal to noise and spectral resolution using the tricorder algorithm

The rapid development of sophisticated imaging spectrometers and resulting flood of imaging spectrometry data has prompted a rapid parallel development of spectral-information extraction technology. Even though these extraction techniques have evolved along different lines (band-shape fitting, endmember unmixing, near-infrared analysis, neural-network fitting, and expert systems to name a few), all are limited by the spectrometer's signal to noise (S/N) and spectral resolution in producing useful information. This study grew from a need to quantitatively determine what effects these parameters have on our ability to differentiate between mineral absorption features using a band-shape fitting algorithm. We chose to evaluate the AVIRIS, HYDICE, MIVIS, GERIS, VIMS, NIMS, and ASTER instruments because they collect data over wide S/N and spectral-resolution ranges. The study evaluates the performance of the Tricorder algorithm, in differentiating between mineral spectra in the 0.4-2.5 micrometer spectral region. The strength of the Tricorder algorithm is in its ability to produce an easily understood comparison of band shape that can concentrate on small relevant portions of the spectra, giving it an advantage over most unmixing schemes, and in that it need not spend large amounts of time reoptimizing each time a new mineral component is added to its reference library, as is the case with neural-network schemes. We believe the flexibility of the Tricorder algorithm is unparalleled among spectral-extraction techniques and that the results from this study, although dealing with minerals, will have direct applications to spectral identification in other disciplines.

Swayze, Gregg A.↗