The VolumePro Volume Rendering Cluster: A Vital Component of Parallel End-to-End Solution

As data sets, both acquired from scanners and those generated from complex simulations, grow in size and complexity, researchers continue to push the boundaries of the amount of data that can be viewed, processed and analyzed interactively. It soon becomes clear that today's algorithms and systems must be scaled through the use of parallelism in order to create viable and cost effective solutions. But for parallelism to be most effective, it must be conceived and designed for efficiency through-out every individual component of the processing and computational pipeline. In fact, a parallel architecture must be preserved throughout the whole process in order to avoid single pipeline bottlenecks

Uintah: a massively parallel problem solving environment

Journal ArticleThis paper describes Uintah, a component-based visual problem solving environment (PSE) that is designed to specifically address the unique problems of massively parallel computation on terascale computing platforms. Uintah supports the entire life cycle of scientific applications by allowing scientific programmers to quickly and easily develop new techniques, debug new implementations, and apply known algorithms to solve novel problems. Uintah is built on three principles: 1) As much as possible, the complexities of parallel execution should be handled for the scientist, 2) software should be reusable at the component level, and 3) scientists should be able to dynamically steer and visualize their simulation results as the simulation executes. To provide this functionality, Uintah builds upon the best features of the SCIRun PSE and the DOE Common Component Architecture (CCA)

Uintah parallelism infrastructure: a performance evaluation on the SGI origin 2000

ManuscriptUintah is a component-based visual problem solving environment (PSE) designed to specifically address the unique problems inherent in running massively parallel scientific computations on terascale computing platforms. In particular, development of the Uintah system is part of the C-SAFE [2] effort to study the interactions between hydrocarbon fires, structures and high-energy materials (explosives and propellants). In this paper we describe methods for generating meaningful performance measurements for the Uintah PSE runing on the SGI Origin 2000 multiprocessor architecture (these methods are applicable to many other applications.) These techniques include utilizing the non-intrusive performance counters built into the R10k and R12k processors, controlling process placement, controlling memory layout, and utilization of a task graph approach to specifying and solving the problem

Finite element anaylsis of non-Darcy flow

This thesis presents the development of a finite element model for unsteady non-Darcy flow. The unsteady flow model is used to solve a free surface flow problem in which the initial conditions are given and the boundary conditions are specified functions of time. The unsteady flow problem is solved in small time steps, At each time step the internal flow is solved by steady flow methods and a Lagrangian technique used to compute the new free surface. A transformation of the dependent variable is proposed in order to account for small inertial effects in tle unsteady flow. The unsteady finite element model is applied to the solution of rapid drawdown in rockfill. There was good agreement between the experimental and computed drawdown profiles. A theoretical evaluation of the unsteady inertial term indicates that this term is only of secondary importance for the material used in the experimental studies, i.e. 1.66 cm and 4.40 cm crushed rock. The finite element solutions, also, indicated that the unsteady inertial term was relatively small compared with frictional resistance. The results of the experimental studies which were carried out to establish flow resistarce equations for the verification studies, are also given. Both parallel and radial flow tests were made. A tendency, for the flow resistance of a material in a converging flow permeameter to be slightly less than for the same material in the parallel flow permeameter, is noted. General flow resistance equations based on the Ward equation and the Kovacs equation are proposed. In the course of developing the unsteady flow finite element models, steady flow finite element models were developed. The steady flow finite element models were also verified experimentally. A brief review of the steady flow development is presented

A study of swirling flow in hydraulic models

In this paper a study is made of vortex behaviour in axially asymmetrical hydraulic models. A brief review of the existing research on vortex models is given. Some of the existing theories have been extended to obtain theoretical descriptions of the vortices studied. The effects of model scale and geometry on vortices with well-developed air cores were investigated experimentally. Three model sizes having 2", 4" and 6" diameter sharp-edged orifices were tested and for each two reservoir configurations (rectangular and 'horsshoe chased) were used. An eccentric inflow produced a reasonably stable swirl. Similarity of swirl production, discharges and air cores has boon considered. It as found that vortex behaviour was sensitive to the irregularity of the model geometry. The vortices in the rectangular models were weaker ah stable than those in the horseshoe shaped models. A general dissimilarity was found between the swirls produced in the smallest model and those in the larger models. The highest swirl numbers 'ere observed in the smallest model. Apart from the above effect, a local scale effect was observed in the region of the air core; the swirl reduction in the region at the air core was greatest in the smallest model. A. theoretical explanation is given for this effect. Most of the experimental work was confined to steady flow at low submergence ratios ((flow depth)/(orifice diameter)<3) in order to obtain reasonably stable well-devloped air cores

Eco-Hydrology Modeling in Coastal Louisiana to Assess Project Effects on the Landscape

Source: ICHE Conference Archive - https://mdi-de.baw.de/icheArchiv

Spatial Distribution of Petroleum Hydrocarbons in Sediment Cores from Blind Pass, St. Pete Beach, Florida

One hundred and one sediment cores were collected to characterize the spatial distribution of petroleum hydrocarbons within and just outside Blind Pass, St. Pete Beach, Florida. Twenty-five percent of the cores exhibited levels of petroleum hydrocarbons above detection limits of the gas chromatograph/flame ionization detector (GC/FID) (0.01 mg/Kg), but at generally low concentrations. Petroleum hydrocarbon speciation studies of these samples (gas chromatography/mass spectroscopy [GC/MS]) indicate above-detection level (1 μg/Kg) petroleum hydrocarbons are similar to the non-volatile petroleum hydrocarbons found in a Bouchard 155 reference sample collected after the 1993 oil spill in the area, but are in a much degraded and weathered state. Individual petroleum hydrocarbons were, in all but one case, below the threshold effective level (TEL) described in the literature (MacDonald, 1994). The petroleum hydrocarbons were primarily found at 100-300 cm depth in Blind Pass cores. Above-detection level petroleum hydrocarbons were generally found in samples from cores in the center of the channel, near the edges of the shoal, and just outside of Blind Pass. A second mixture of hydrocarbons, primarily phthalates, ketones, and ether, was found at relatively shallow core depths (0-99 cm) in the Mid- and North End Channel cores. These suggest a separate source of contamination, possibly storm water runoff. The fuel fluorescence detector (FFD) probe was investigated for its ability to detect petroleum hydrocarbons in marine sediments. When analyzed with the FFD, all sediments from the cores produced peaks of fluorescence, but none above the background levels of Blind Pass native sediments. All but two samples analyzed by GC/FID were below the detection limits (100 ppm) of the FFD. These samples were found in dark-colored sediments. The combination of the detection limits of the instrument, sediment color, and the degraded nature of the heavier weight petroleum hydrocarbons may have resulted in fluorescence outputs below background levels. These studies demonstrate that the distribution of petroleum hydrocarbons within Blind Pass sediments is generally low and patchy. However, 25% of the cores exhibited levels above detection using GC/FID/MS. These cores could be subjected to individual speciation studies which indicate generally below TEL levels and an association of some, but not all, with the 1993 oil spill in Blind Pass. Appendix A provides photographs and tables for sediment subsamples which exhibited total petroleum hydrocarbon concentrations above detection limits, while Appendix B presents the results from fuel fluorescence detector probe analyses. A discussion of the results of the study in relation to sediment quality guidelines and soil cleanup target level guidance documents is included as Appendix C. Some preliminary results using the above techniques on core samples from the nearby John’s Pass are presented in Appendix D

Altered microRNA expression in frontotemporal lobar degeneration with TDP-43 pathology caused by progranulin mutations

<p>Abstract</p> <p>Background</p> <p>Frontotemporal lobar degeneration (FTLD) is a progressive neurodegenerative disorder that can be triggered through genetic or sporadic mechanisms. MicroRNAs (miRNAs) have become a major therapeutic focus as their pervasive expression and powerful regulatory roles in disease pathogenesis become increasingly apparent. Here we examine the role of miRNAs in FTLD patients with TAR DNA-binding protein 43 pathology (FTLD-TDP) caused by genetic mutations in the progranulin (<it>PGRN</it>) gene.</p> <p>Results</p> <p>Using miRNA array profiling, we identified the 20 miRNAs that showed greatest evidence (unadjusted P < 0.05) of dysregulation in frontal cortex of eight FTLD-TDP patients carrying <it>PGRN </it>mutations when compared to 32 FTLD-TDP patients with no apparent genetic abnormalities. Quantitative real-time PCR (qRT-PCR) analyses provided technical validation of the differential expression for 9 of the 20 miRNAs in frontal cortex. Additional qRT-PCR analyses showed that 5 out of 9 miRNAs (miR-922, miR-516a-3p, miR-571, miR-548b-5p, and miR-548c-5p) were also significantly dysregulated (unadjusted P < 0.05) in cerebellar tissue samples of <it>PGRN </it>mutation carriers, consistent with a systemic reduction in PGRN levels. We developed a list of gene targets for the 5 candidate miRNAs and found 18 genes dysregulated in a reported FTLD mRNA study to exhibit anti-correlated miRNA-mRNA patterns in affected cortex and cerebellar tissue. Among the targets is brain-specific angiogenesis inhibitor 3, which was recently identified as an important player in synapse biology.</p> <p>Conclusions</p> <p>Our study suggests that miRNAs may contribute to the pathogenesis of FTLD-TDP caused by <it>PGRN </it>mutations and provides new insight into potential future therapeutic options.</p