Remote Object Detection in Cluster-Based Java

Our work combines Java compilation to native code with a run-time library that executes Java threads in a distributed-memory environment with true parallelism. This approach is implemented within the Hyperion system for the distributed execution of compiled Java programs on clusters of PCs. To provide the illusion of a shared memory to Java threads, Hyperion has been built on top of DSM-PM2, a portable implementation platform for multithreaded distributed-shared-memory protocols. We have designed, implemented and experimented with two alternative consistency protocols compliant with the Java Memory Model. The protocols have different mechanisms for access detection: the first one uses explicit locality checks, whereas the second one is based on page faults. We illustrate the effects of the two access-detection techniques with five applications run on two clusters with different interconnection networks: BIP/Myrinet and SISCI/SCI.Notre travail étudie la compilation de programmes Java vers du code natif, en présence d'une bibliothèque run-time permettant des threads Java de s'exécuter en environnement à mémoire distribuée avec du vrai parallélisme. Pour fournir aux threads Java l'illusion d'une mémoire partagée, notre système de compilation '(appelé Hypérion) a été conçu au-dessus de DSm-PM2, une plateforme portable qui facilite l'implémentation de protocoles de cohérence multi-thread pour des systèmes à mémoire distribuée virtuellement partagée. Nous avons conçu, implémenté et expérimenté deux protocole de cohérence alternatifs, compatibles avec le modèle de mémoire Java (Java Memory Model). Les protocoles utilisent des mécanismes différents pour la détection d'accès aux objets partagés. Nous illustrons les effets des deux techniques de détection d'accès à l'aide de cinq applications exécutées sur deux grappes comportant des réseaux d'interconnexion différents : BIP/Myrinet et SISCI/SC

Binary Adaptive Semi-Global Matching Based on Image Edges

Image-based modeling and rendering is currently one of the most challenging topics in Computer Vision and Photogrammetry. The key issue here is building a set of dense correspondence points between two images, namely dense matching or stereo matching. Among all dense matching algorithms, Semi-Global Matching (SGM) is arguably one of the most promising algorithms for real-time stereo vision. Compared with global matching algorithms, SGM aggregates matching cost from several (eight or sixteen) directions rather than only the epipolar line using Dynamic Programming (DP). Thus, SGM eliminates the classical “streaking problem” and greatly improves its accuracy and efficiency. In this paper, we aim at further improvement of SGM accuracy without increasing the computational cost. We propose setting the penalty parameters adaptively according to image edges extracted by edge detectors. We have carried out experiments on the standard Middlebury stereo dataset and evaluated the performance of our modified method with the ground truth. The results have shown a noticeable accuracy improvement compared with the results using fixed penalty parameters while the runtime computational cost was not increased

Evolutionary rates and gene dispensability associate with replication timing in the Archaeon Sulfolobus islandicus

In bacterial chromosomes, the position of a gene relative to the single origin of replication generally reflects its replication timing, how often it is expressed, and consequently, its rate of evolution. However, because some archaeal genomes contain multiple origins of replication, bias in gene dosage caused by delayed replication should be minimized and hence the substitution rate of genes should associate less with chromosome position. To test this hypothesis, six archaeal genomes from the genus Sulfolobus containing three origins of replication were selected, conserved orthologs were identified, and the evolutionary rates (dN and dS) of these orthologs were quantified. Ortholog families were grouped by their consensus position and designated by their proximity to one of the three origins (O1, O2, O3). Conserved orthologs were concentrated near the origins and most variation in genome content occurred distant from the origins. Linear regressions of both synonymous and nonsynonymous substitution rates on distance from replication origins were significantly positive, the rates being greatest in the region furthest from any of the origins and slowest among genes near the origins. Genes near O1 also evolved faster than those near O2 and O3, which suggest that this origin may fire later in the cell cycle. Increased evolutionary rates and gene dispensability are strongly associated with reduced gene expression caused in part by reduced gene dosage during the cell cycle. Therefore, in this genus of Archaea as well as in many Bacteria, evolutionary rates and variation in genome content associate with replication timing

Why genes evolve faster on secondary chromosomes in bacteria

In bacterial genomes composed of more than one chromosome, one replicon is typically larger, harbors more essential genes than the others, and is considered primary. The greater variability of secondary chromosomes among related taxa has led to the theory that they serve as an accessory genome for specific niches or conditions. By this rationale, purifying selection should be weaker on genes on secondary chromosomes because of their reduced necessity or usage. To test this hypothesis we selected bacterial genomes composed of multiple chromosomes from two genera, Burkholderia and Vibrio, and quantified the evolutionary rates (dN and dS) of all orthologs within each genus. Both evolutionary rate parameters were faster among orthologs found on secondary chromosomes than those on the primary chromosome. Further, in every bacterial genome with multiple chromosomes that we studied, genes on secondary chromosomes exhibited significantly weaker codon usage bias than those on primary chromosomes. Faster evolution and reduced codon bias could in turn result from global effects of chromosome position, as genes on secondary chromosomes experience reduced dosage and expression due to their delayed replication, or selection on specific gene attributes. These alternatives were evaluated using orthologs common to genomes with multiple chromosomes and genomes with single chromosomes. Analysis of these ortholog sets suggested that inherently fast-evolving genes tend to be sorted to secondary chromosomes when they arise; however, prolonged evolution on a secondary chromosome further accelerated substitution rates. In summary, secondary chromosomes in bacteria are evolutionary test beds where genes are weakly preserved and evolve more rapidly, likely because they are used less frequently

Comparative genomics of Burkholderia multivorans, a ubiquitous pathogen with a highly conserved genomic structure

The natural environment serves as a reservoir of opportunistic pathogens. A well-established method for studying the epidemiology of such opportunists is multilocus sequence typing, which in many cases has defined strains predisposed to causing infection. Burkholderia multivorans is an important pathogen in people with cystic fibrosis (CF) and its epidemiology suggests that strains are acquired from non-human sources such as the natural environment. This raises the central question of whether the isolation source (CF or environment) or the multilocus sequence type (ST) of B. multivorans better predicts their genomic content and functionality. We identified four pairs of B. multivorans isolates, representing distinct STs and consisting of one CF and one environmental isolate each. All genomes were sequenced using the PacBio SMRT sequencing technology, which resulted in eight high-quality B. multivorans genome assemblies. The present study demonstrated that the genomic structure of the examined B. multivorans STs is highly conserved and that the B. multivorans genomic lineages are defined by their ST. Orthologous protein families were not uniformly distributed among chromosomes, with core orthologs being enriched on the primary chromosome and ST-specific orthologs being enriched on the second and third chromosome. The ST-specific orthologs were enriched in genes involved in defense mechanisms and secondary metabolism, corroborating the strain-specificity of these virulence characteristics. Finally, the same B. multivorans genomic lineages occur in both CF and environmental samples and on different continents, demonstrating their ubiquity and evolutionary persistence

Investigating the cause for the increase in the atmospheric methane burden from 2007 to present

The global atmospheric methane burden approached equilibrium from 1983 until 2006, after which there was an increase in the rate of change that’s been sustained since then. It’s uncertain if this change was due to an increase in emissions, or a decrease in the rate of sink, or a combination of both. Our method attempted to provide evidence to show whether or not this change was due to a decrease in the sink, corresponding to an increase in the lifetime of methane. A one-box model of methane was employed to determine what the lifetime of methane would need to be each year if emissions were held constant. The primary loss mechanism for methane is the same for carbon monoxide: reactions with hydroxyl radicals. If there was a change in the sink for methane, it’s very likely that this would be due to a change in the concentration of hydroxyl. It was shown that the corresponding change in carbon monoxide concentrations would be insignificant compared to the variability of the observations. This insignificant change renders our method inconclusive

Sustain SLO Undergraduate Narrative Research: Reenergizing Learning

This proposal would allow four undergraduate students to present their research paper on transformative learning at an American Society of Engineering Education (ASEE) conference in Seattle in June 2015. These four students participated in SUSTAIN SLO, a community-based learning initiative, their freshman year at Cal Poly. SUSTAIN SLO is sponsored by the National Science Foundation to study aspects of change in higher education. As part of SUSTAIN\u27s research, 23 students who participated in the first generation of the initiative in 2012 were interviewed one year after their experience. During summer 2014, the four undergraduate students involved in this proposal partnered with Liz Schlemer, IME professor and co-PI of SUSTAIN, to quantitatively analyze these narratives to explore these two questions: 1) How is SUSTAIN different than the traditional course experience? and 2) How did SUSTAIN affect you? This team of 4 undergraduate students and 1 professor is currently in the process of writing their findings and will submit their paper to the ASEE in January 2015. The funds requested in this proposal would cover the cost of plane tickets, hotel rooms, and conference registration fees

Small deformations of spherical biomembranes

In this contribution to the proceedings of the 11th Mathematical Society of Japan (MSJ) Seasonal Institute (July 2018) we give an overview of some recent work on a mathematical model for small deformations of a spherical membrane. The idea is to consider perturbations to minimisers of a surface geometric energy. The model is obtained from consideration of second order approximations to a perturbed energy. In particular, the considered problems involve particle constraints and surface phase field energies.Comment: Submission to the proceedings of the 11th Mathematical Society of Japan (MSJ) Seasonal Institute (July 2018

The Hyperion system: Compiling multithreaded Java bytecode for distributed execution

A preliminary version of this work has been presented as a Distinguished Paper at the Euro-Par 2000 Conference, Munich, Germany, August 2000.International audienceOur work combines Java compilation to native code with a runtime library that executes Java threads in a distributed memory environment. This allows a Java programmer to view a cluster of processors as executing a single JAVA virtual machine. The separate processors are simply resources for executing Java threads with true parallelism, and the run-time system provides the illusion of a shared memory on top of the private memories of the processors. The environment we present is available on top of several UNIX systems and can use a large variety of communication interfaces thanks to the high portability of its run time system. To evaluate our approach, we compare serial C, serial Java, and multithreaded Java implementations of a branch and-bound solution to the minimal-cost map-coloring problem. All measurements have been carried out on two platforms using two different communication interfaces: SISCI/SCI and MPI BIP/Myrinet