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At least 775 records · Page 43

The VTK-m Users' Guide (V.2.0)

High-performance computing relies on ever finer threading. Advances in processor technology include ever greater numbers of cores, hyperthreading, accelerators with integrated blocks of cores, and special vectorized instructions, all of which require more software parallelism to achieve peak performance. Traditional visualization solutions cannot support this extreme level of concurrency. Extreme scale systems require a new programming model and a fundamental change in how we design algorithms. To address these issues we created VTK-m: the visualization toolkit for multi-/many-core architectures. VTK-m supports a number of algorithms and the ability to design further algorithms through a top-down design with an emphasis on extreme parallelism. VTK-m also provides support for finding and building links across topologies, making it possible to perform operations that determine manifold surfaces, interpolate generated values, and find adjacencies. Although VTK-m provides a simplified high-level interface for programming, its template-based code removes the overhead of abstraction. VTK-m simplifies the development of parallel scientific visualization algorithms by providing a framework of supporting functionality that allows developers to focus on visualization operations. Consider the listings in Figure 1.1 that compares the size of the implementation for the Marching Cubes algorithm in VTK-m with the equivalent reference implementation in the CUDA software development kit. Because VTK-m internally manages the parallel distribution of work and data, the VTK-m implementation is shorter and easier to maintain. Additionally, VTK-m provides data abstractions not provided by other libraries that make code written in VTK-m more versatile.

97 MATHEMATICS AND COMPUTING↗

MPI nuts and bolts and more [Slides]

MPI (Message-Passing Interface) is a message-passing library interface specification. All parts of this definition are significant. MPI addresses primarily the message-passing parallel programming model, in which data is moved from the address space of one process to that of another process through cooperative operations on each process. . . MPI is a specification, not an implementation; there are multiple implementations of MPI. This specification is for a library interface; MPI is not a language, and all MPI operations are expressed as functions, subroutines, or methods, according to the appropriate language bindings that, for C and Fortran, are part of the MPI standard. MPI Forum is the organization which is responsible for the MPI Specification.

97 MATHEMATICS AND COMPUTING↗

New Results on Communication- and Memory-Aware Load Balancing Model and Algorithms

While load balancing in distributed-memory computing has been well-studied, we present an innovative approach to this problem: a unified, reduced-order model that combines three key components to describe “work” in a distributed system: computation, communication, and memory. Our model enables an optimizer to explore complex tradeoffs in task placement, such as augmented parallelism, at the expense of data replication increasing memory usage. We propose a fully distributed, heuristic-based load balancing optimization algorithm, and demonstrate that it quickly finds close-to-optimal solutions. We formalize the complex optimization problem as a mixed-integer linear program, and compare it to our strategy. Finally, we show that when applied to an electromagnetics code, our approach obtains up to 2.3x speedups for the imbalanced execution.

97 MATHEMATICS AND COMPUTING↗

Chromatin Changes in Phytochrome Interacting Factor-Regulated Genes Parallel Their Rapid Transcriptional Response to Light

As sessile organisms, plants must adapt to a changing environment, sensing variations in resource availability and modifying their development in response. Light is one of the most important resources for plants, and its perception by sensory photoreceptors (e.g., phytochromes) and subsequent transduction into long-term transcriptional reprogramming have been well characterized. Chromatin changes have been shown to be involved in photomorphogenesis. However, the initial short-term transcriptional changes produced by light and what factors enable these rapid changes are not well studied. Here, we define rapidly light-responsive, Phytochrome Interacting Factor (PIF) direct-target genes (LRP-DTGs). We found that a majority of these genes also show rapid changes in Histone 3 Lysine-9 acetylation (H3K9ac) in response to the light signal. Detailed time-course analysis of transcript and chromatin changes showed that, for light-repressed genes, H3K9 deacetylation parallels light-triggered transcriptional repression, while for light-induced genes, H3K9 acetylation appeared to somewhat precede light-activated transcript accumulation. However, direct, real-time imaging of transcript elongation in the nucleus revealed that, in fact, transcriptional induction actually parallels H3K9 acetylation. Collectively, the data raise the possibility that light-induced transcriptional and chromatin-remodeling processes are mechanistically intertwined. Histone modifying proteins involved in long term light responses do not seem to have a role in this fast response, indicating that different factors might act at different stages of the light response. This work not only advances our understanding of plant responses to light, but also unveils a system in which rapid chromatin changes in reaction to an external signal can be studied under natural conditions.

59 BASIC BIOLOGICAL SCIENCES↗

Digital interactive image analysis by array processing

An attempt is made to draw a parallel between the existing geophysical data processing service industries and the emerging earth resources data support requirements. The relationship of seismic data analysis to ERTS data analysis is natural because in either case data is digitally recorded in the same format, resulting from remotely sensed energy which has been reflected, attenuated, shifted and degraded on its path from the source to the receiver. In the seismic case the energy is acoustic, ranging in frequencies from 10 to 75 cps, for which the lithosphere appears semi-transparent. In earth survey remote sensing through the atmosphere, visible and infrared frequency bands are being used. Yet the hardware and software required to process the magnetically recorded data from the two realms of inquiry are identical and similar, respectively. The resulting data products are similar.

Sabels, B. E.↗

The average auroral zone electric field

Four hundred and seventy-eight hours of electric field data obtained by the flight of 32 balloons between L = 5.4 and L = 8.2 have been averaged to determine mean properties of the auroral zone electric field. The results are understood in terms of a model in which the two-cell convection pattern is rotated about the sun-earth line by an amount that depends on the sign and magnitude of the y component of the interplanetary magnetic field. This model and the data suggest either that important parallel potential drops exist along auroral zone magnetic field lines or that simple conjugacy between the two hemispheres does not exist along such field lines.

Mozer, F. S.↗

Multiple detector focal plane array ultraviolet spectrometer for the AMPS laboratory

The possibility of meeting the requirements of the amps spectroscopic instrumentation by using a multi-element focal plane detector array in a conventional spectrograph mount was examined. The requirements of the detector array were determined from the optical design of the spectrometer which in turn depends on the desired level of resolution and sensitivity required. The choice of available detectors and their associated electronics and controls was surveyed, bearing in mind that the data collection rate from this system is so great that on-board processing and reduction of data are absolutely essential. Finally, parallel developments in instrumentation for imaging in astronomy were examined, both in the ultraviolet (for the Large Space Telescope as well as other rocket and satellite programs) and in the visible, to determine what progress in that area can have direct bearing on atmospheric spectroscopy.

Feldman, P. D.↗

Storage of solid propellants in space

A test program is described which determines the extent of physical property changes that result from extended space exposure. Primary emphasis was placed on determining the effects of space vacuum. Solid propellants were stored and their physical properties tested in a vacuum and in a dry environment. The storage caused significantly greater increases in the propellants' modulus and maximum tensile strength than occurred in parallel ambient stored samples. The data indicate that the loss of trace amounts of residual moisture from cured propellant is the apparent cause of the observed propellant property changes. Therefore, initial screening tests were carried out under dry storage conditions. Upon completion of the dry storage tests, appropriate propellant samples are exposed to an actual space environment using the Long Duration Exposure Facility (LDEF).

Udlock, D. E.↗

Computational methods for analyzing the transmission characteristics of a beta particle magnetic analysis system

Computational methods were developed to study the trajectories of beta particles (positrons) through a magnetic analysis system as a function of the spatial distribution of the radionuclides in the beta source, size and shape of the source collimator, and the strength of the analyzer magnetic field. On the basis of these methods, the particle flux, their energy spectrum, and source-to-target transit times have been calculated for Na-22 positrons as a function of the analyzer magnetic field and the size and location of the target. These data are in studies requiring parallel beams of positrons of uniform energy such as measurement of the moisture distribution in composite materials. Computer programs for obtaining various trajectories are included.

Singh, J. J.↗

On the polarization state of hydromagnetic fluctuations in the solar wind

From presently available observations it can be inferred that the Alfvenic turbulence measured in the solar wind, predominantly on trailing edges of high speed streams, is a mixture of modes with two different polarizations, namely, Alfvenic modes and modes which are the incompressible limit of slow magnetosonic waves. Using Helios 2 magnetic data and a variance analysis, parallel (to the mean field) and perpendicular components of the fluctuations are separated and the possible correlation between such components is studied. Correlations between eigenvalues of the variance matrix are also investigated and discussed.

Bavassano, B.↗

Fiber optics for aircraft engine/inlet control

NASA programs that focus on the use of fiber optics for aircraft engine/inlet control are reviewed. Fiber optics for aircraft control is attractive because of its inherent immunity to EMI and RFI noise. Optical signals can be safely transmitted through areas that contain flammable or explosive materials. The use of optics also makes remote sensing feasible by eliminating the need for electrical wires to be connected between sensors and computers. Using low-level optical signals to control actuators is also feasible when power is generated at the actuator. Each application of fiber optics for aircraft control has different requirements for both the optical cables and the optical connectors. Sensors that measure position and speed by using slotted plates can use lossy cables and bundle connectors if data transfer is in the parallel mode. If position and speed signals are multiplexed, cable and connector requirements change. Other sensors that depend on changes in transmission through materials require dependable characteristics of both the optical cables and the optical connectors. A variety of sensor types are reviewed, including rotary position encoders, tachometers, temperature sensors, and blade tip clearance sensors for compressors and turbines. Research on a gallium arsenide photoswitch for optically switched actuators that operate at 250 C is also described.

Baumbick, R. J.↗

On the polarization state of hydromagnetic fluctuations in the solar wind

From presently available observations one can infer that the Alfvenic turbulence measured in the solar wind, predominantly on trailing edges of high-speed streams, is a mixture of modes with two different polarizations, namely, Alfvenic modes and modes which are the incompressible limit of slow magnetosonic waves. Using Helios 2 magnetic data and a variance analysis, parallel (to the mean field) and perpendicular components of the fluctuations are separated, and the possible correlation between such components which would be predicted as a consequence of the incompressible character of the turbulence is studied. Correlations between eigenvalues of the variance matrix are also investigated and discussed.

Bavassano, B.↗

Solid-propellant rocket motor internal ballistics performance variation analysis, phase 5

The results of research aimed at improving the predictability of internal ballistics performance of solid-propellant rocket motors (SRM's) including thrust imbalance between two SRM's firing in parallel are presented. Static test data from the first six Space Shuttle SRM's is analyzed using a computer program previously developed for this purpose. The program permits intentional minor design biases affecting the imbalance between any two SMR's to be removed. Results for the last four of the six SRM's, with only the propellant bulk temperature as a non-random variable, are generally within limits predicted by theory. Extended studies of internal ballistic performance of single SRM's are presented based on an earlier developed mathematical model which includes an assessment of grain deformation. The erosive burning rate law used in the model is upgraded and made more general. Excellent results are obtained in predictions of the performances of five different SRM's of quite different sizes and configurations. These SRM's all employ PBAN type propellants with ammonium perchlorate oxidizer and 16 to 20% aluminum except one which uses carboxyl terminated butadiene binder. The only non-calculated parameters in the burning rate equations that are changed for the different SRM's are the zero crossflow velocity burning rate coefficients and exponents. The results, in general, confirm the importance of grain deformation. The improved internal ballistic model makes practical development of an effective computer program for application of an optimization technique to SRM design which is also demonstrated. The program uses a pattern search technique to minimize the difference between a desired thrust-time trace and one calculated based on the internal ballistic model.

Sforzini, R. H.↗

Earth's compressional foreshock boundary revisited Observations by the ISEE 1 magnetometer

A 'solar foreshock coordinate' (SFC) system is introduced in which the positions of foreshock components can be collated with a minimum of assumptions about the physical processes involved. Location behind the interplanetary magnetic field (IMF) tangent surface to the bow shock and rotational symmetry around the solar wind flow (X) axis are the only presuppositions. The SFC system has been applied to over 300 observations of the boundary of the ULF compressional waves recorded by ISEE 1's magnetometer in 1978 and 1979. The boundary locations form a coherent pattern in the SFC frame. A selection of those cases for which the cone angle of the IMF was between 40 and 50 deg, corresponding to the average stream angle, yields a least square line whose mapping back to the solar ecliptic coordinates frame has slope of about 85 deg, very close to that of the tangent ULF boundary deduced earlier from more primitive methods with entirely different data sets. The line, being parallel to neither the IMF, the typical reflected beam, nor the shock, cannot be compatible with any model of wave production by beam-solar wind interaction that depends on uniform beam distribution or fixed growth rate. Rather, its tangency suggests the influence of a separate, escaping ion population.

Greenstadt, E. W.↗

Why does near ridge extensional seismicity occur primarily in the Indian Ocean?

It is argued that though thermoelastic stresses provide a low level background in all plates, the data favoring their contributing significantly to the stress field and seismicity in the young oceanic lithosphere may be interpreted in terms of stresses resulting from individual plate geometry and local boundary effects. The dramatic concentration of extensional seismicity in the Central Indian Ocean region is shown to be consistent with finite element results for the intraplate stress incorporating the effects of the Himalayan collision and the various subduction zones. Most of the data for both ridge-parallel extension and depth stratification are provided by earthquakes in this area, and it is suggested that these effects may be due more to the regional stress.

Stein, Seth↗

Electronic Neural Networks

Memory based on neural network models content-addressable and fault-tolerant. System includes electronic equivalent of synaptic network; particular, matrix of programmable binary switching elements over which data distributed. Switches programmed in parallel by outputs of serial-input/parallel-output shift registers. Input and output terminals of bank of high-gain nonlinear amplifiers connected in nonlinear-feedback configuration by switches and by memory-prompting shift registers.

Lambe, John↗

Parallel processors and nonlinear structural dynamics algorithms and software

The adaptation of a finite element program with explicit time integration to a massively parallel SIMD (single instruction multiple data) computer, the CONNECTION Machine is described. The adaptation required the development of a new algorithm, called the exchange algorithm, in which all nodal variables are allocated to the element with an exchange of nodal forces at each time step. The architectural and C* programming language features of the CONNECTION Machine are also summarized. Various alternate data structures and associated algorithms for nonlinear finite element analysis are discussed and compared. Results are presented which demonstrate that the CONNECTION Machine is capable of outperforming the CRAY XMP/14.

Belytschko, Ted↗

Line-drawing algorithms for parallel machines

The fact that conventional line-drawing algorithms, when applied directly on parallel machines, can lead to very inefficient codes is addressed. It is suggested that instead of modifying an existing algorithm for a parallel machine, a more efficient implementation can be produced by going back to the invariants in the definition. Popular line-drawing algorithms are compared with two alternatives; distance to a line (a point is on the line if sufficiently close to it) and intersection with a line (a point on the line if an intersection point). For massively parallel single-instruction-multiple-data (SIMD) machines (with thousands of processors and up), the alternatives provide viable line-drawing algorithms. Because of the pixel-per-processor mapping, their performance is independent of the line length and orientation.

Pang, Alex T.↗