Performance analysis and tuning in multicore environments

Performance analysis is the task of monitor the behavior of a program execution. The main goal is to find out the possible adjustments that might be done in order improve the performance. To be able to get that improvement it is necessary to find the different causes of overhead. Nowadays we are already in the multicore era, but there is a gap between the level of development of the two main divisions of multicore technology (hardware and software). When we talk about multicore we are also speaking of shared memory systems, on this master thesis we talk about the issues involved on the performance analysis and tuning of applications running specifically in a shared Memory system. We move one step ahead to take the performance analysis to another level by analyzing the applications structure and patterns. We also present some tools specifically addressed to the performance analysis of OpenMP multithread application. At the end we present the results of some experiments performed with a set of OpenMP scientific application.

Switching between apparently redundant iron-uptake mechanisms benefits bacteria in changeable environments.

Bacteria often possess multiple siderophore-based iron uptake systems for scavenging this vital resource from their environment. However, some siderophores seem redundant, because they have limited iron-binding efficiency and are seldom expressed under iron limitation. Here, we investigate the conundrum of why selection does not eliminate this apparent redundancy. We focus on Pseudomonas aeruginosa, a bacterium that can produce two siderophores-the highly efficient but metabolically expensive pyoverdine, and the inefficient but metabolically cheap pyochelin. We found that the bacteria possess molecular mechanisms to phenotypically switch from mainly producing pyoverdine under severe iron limitation to mainly producing pyochelin when iron is only moderately limited. We further show that strains exclusively producing pyochelin grew significantly better than strains exclusively producing pyoverdine under moderate iron limitation, whereas the inverse was seen under severe iron limitation. This suggests that pyochelin is not redundant, but that switching between siderophore strategies might be beneficial to trade off efficiencies versus costs of siderophores. Indeed, simulations parameterized from our data confirmed that strains retaining the capacity to switch between siderophores significantly outcompeted strains defective for one or the other siderophore under fluctuating iron availabilities. Finally, we discuss how siderophore switching can be viewed as a form of collective decision-making, whereby a coordinated shift in behaviour at the group level emerges as a result of positive and negative feedback loops operating among individuals at the local scale.

Occurrence of Plesiomonas shigelloides in water environments of Rio de Janeiro city

Fresh and salt water samples analyzed in Rio de Janeiro city showed the presence of Plesiomonas shigelloides. Forty-six strains were isolated from both environments. A high incidence of P. shigelloides was achieved in polluted fresh and salt waters as well as in samples from non-polluted streams. P. shigelloides isolates had biochemical characteristics similar to those already described in the literature. None of the isolates analyzed produced enterotoxin in the suckling mouse assay. Hemolytic activity against sheep and human type A erythrocytes was detected in the strains tested. The results of the antibiotic susceptibility tests indicated that all the isolates were susceptible to the cephalosporins, penicillins combined with a beta-lactamase inhibitor, aminoglycosides, imipenem, norfloxacin, tetracycline, chloramphenicol and trimethoprim-sulfamethoxazole. All the isolates were resistant to the penicillins.

Ecology of Triatoma rubrovaria (Hemiptera, Triatominae) in wild and peridomestic environments of Uruguay

This paper describes population structure, spatial distribution and habitat selection of wild and peridomestic populations of Triatoma rubrovaria (Blanchard, 1843). Field studies were carried out at Las Piedras and La Bolsa in the Northern Department of Artigas, Uruguay. A semicircular sampling area, divided in seven or eight triangular sectors was sequentially examined from October 1990 to November 1991. At Las Piedras (typical wild habitat) 1063 T. rubrovaria bugs were collected from 84 of the rocky outcroops ("pedregales"). Abundance varied by season peaking in October-November (spring). Throughout the year, most of the population was made up of third, fourth and fifth instar nymphs; adults were found from October to March. In the peridomestic environment of La Bolsa, however T. rubrovaria was less common and showed a more irregular instar distribution. Colonized ecotopes, were those close to houses. In both sites T. rubrovaria was mainly associated with the geckonid Homonota uruguayensis and the cockroach Blaptica dubia.

Evolution of decision-making and learning under fluctuating social environments

The capacity to learn to associate sensory perceptions with appropriate motor actions underlies the success of many animal species, from insects to humans. The evolutionary significance of learning has long been a subject of interest for evolutionary biologists who emphasize the bene¬fit yielded by learning under changing environmental conditions, where it is required to flexibly switch from one behavior to another. However, two unsolved questions are particularly impor¬tant for improving our knowledge of the evolutionary advantages provided by learning, and are addressed in the present work. First, because it is possible to learn the wrong behavior when a task is too complex, the learning rules and their underlying psychological characteristics that generate truly adaptive behavior must be identified with greater precision, and must be linked to the specific ecological problems faced by each species. A framework for predicting behavior from the definition of a learning rule is developed here. Learning rules capture cognitive features such as the tendency to explore, or the ability to infer rewards associated to unchosen actions. It is shown that these features interact in a non-intuitive way to generate adaptive behavior in social interactions where individuals affect each other's fitness. Such behavioral predictions are used in an evolutionary model to demonstrate that, surprisingly, simple trial-and-error learn¬ing is not always outcompeted by more computationally demanding inference-based learning, when population members interact in pairwise social interactions. A second question in the evolution of learning is its link with and relative advantage compared to other simpler forms of phenotypic plasticity. After providing a conceptual clarification on the distinction between genetically determined vs. learned responses to environmental stimuli, a new factor in the evo¬lution of learning is proposed: environmental complexity. A simple mathematical model shows that a measure of environmental complexity, the number of possible stimuli in one's environ¬ment, is critical for the evolution of learning. In conclusion, this work opens roads for modeling interactions between evolving species and their environment in order to predict how natural se¬lection shapes animals' cognitive abilities. - La capacité d'apprendre à associer des sensations perceptives à des actions motrices appropriées est sous-jacente au succès évolutif de nombreuses espèces, depuis les insectes jusqu'aux êtres hu¬mains. L'importance évolutive de l'apprentissage est depuis longtemps un sujet d'intérêt pour les biologistes de l'évolution, et ces derniers mettent l'accent sur le bénéfice de l'apprentissage lorsque les conditions environnementales sont changeantes, car dans ce cas il est nécessaire de passer de manière flexible d'un comportement à l'autre. Cependant, deux questions non résolues sont importantes afin d'améliorer notre savoir quant aux avantages évolutifs procurés par l'apprentissage. Premièrement, puisqu'il est possible d'apprendre un comportement incorrect quand une tâche est trop complexe, les règles d'apprentissage qui permettent d'atteindre un com¬portement réellement adaptatif doivent être identifiées avec une plus grande précision, et doivent être mises en relation avec les problèmes écologiques spécifiques rencontrés par chaque espèce. Un cadre théorique ayant pour but de prédire le comportement à partir de la définition d'une règle d'apprentissage est développé ici. Il est démontré que les caractéristiques cognitives, telles que la tendance à explorer ou la capacité d'inférer les récompenses liées à des actions non ex¬périmentées, interagissent de manière non-intuitive dans les interactions sociales pour produire des comportements adaptatifs. Ces prédictions comportementales sont utilisées dans un modèle évolutif afin de démontrer que, de manière surprenante, l'apprentissage simple par essai-et-erreur n'est pas toujours battu par l'apprentissage basé sur l'inférence qui est pourtant plus exigeant en puissance de calcul, lorsque les membres d'une population interagissent socialement par pair. Une deuxième question quant à l'évolution de l'apprentissage concerne son lien et son avantage relatif vis-à-vis d'autres formes plus simples de plasticité phénotypique. Après avoir clarifié la distinction entre réponses aux stimuli génétiquement déterminées ou apprises, un nouveau fac¬teur favorisant l'évolution de l'apprentissage est proposé : la complexité environnementale. Un modèle mathématique permet de montrer qu'une mesure de la complexité environnementale - le nombre de stimuli rencontrés dans l'environnement - a un rôle fondamental pour l'évolution de l'apprentissage. En conclusion, ce travail ouvre de nombreuses perspectives quant à la mo¬délisation des interactions entre les espèces en évolution et leur environnement, dans le but de comprendre comment la sélection naturelle façonne les capacités cognitives des animaux.

Entorns col•laboratius virtuals asíncrons basats en Web i enfocats en la gestió del coneixement = Web-based Asynchronous Collaborative Environments Focused on Knowledge Management

Report for the scientific sojourn at the University of California at Berkeley, USA, from september 2007 until july 2008. Communities of Learning Practice is an innovative paradigm focused on providing appropriate technological support to both formal and especially informal learning groups who are chiefly formed by non-technical people and who lack of the necessary resources to acquire such systems. Typically, students who are often separated by geography and/or time have the need to meet each other after classes in small study groups to carry out specific learning activities assigned during the formal learning process. However, the lack of suitable and available groupware applications makes it difficult for these groups of learners to collaborate and achieve their specific learning goals. In addition, the lack of democratic decision-making mechanisms is a main handicap to substitute the central authority of knowledge presented in formal learning.

An efficient use of virtualization in grid/cloud environments

Grid is a hardware and software infrastructure that provides dependable, consistent, pervasive, and inexpensive access to high-end computational resources. Grid enables access to the resources but it does not guarantee any quality of service. Moreover, Grid does not provide performance isolation; job of one user can influence the performance of other user’s job. The other problem with Grid is that the users of Grid belong to scientific community and the jobs require specific and customized software environment. Providing the perfect environment to the user is very difficult in Grid for its dispersed and heterogeneous nature. Though, Cloud computing provide full customization and control, but there is no simple procedure available to submit user jobs as in Grid. The Grid computing can provide customized resources and performance to the user using virtualization. A virtual machine can join the Grid as an execution node. The virtual machine can also be submitted as a job with user jobs inside. Where the first method gives quality of service and performance isolation, the second method also provides customization and administration in addition. In this thesis, a solution is proposed to enable virtual machine reuse which will provide performance isolation with customization and administration. The same virtual machine can be used for several jobs. In the proposed solution customized virtual machines join the Grid pool on user request. Proposed solution describes two scenarios to achieve this goal. In first scenario, user submits their customized virtual machine as a job. The virtual machine joins the Grid pool when it is powered on. In the second scenario, user customized virtual machines are preconfigured in the execution system. These virtual machines join the Grid pool on user request. Condor and VMware server is used to deploy and test the scenarios. Condor supports virtual machine jobs. The scenario 1 is deployed using Condor VM universe. The second scenario uses VMware-VIX API for scripting powering on and powering off of the remote virtual machines. The experimental results shows that as scenario 2 does not need to transfer the virtual machine image, the virtual machine image becomes live on pool more faster. In scenario 1, the virtual machine runs as a condor job, so it easy to administrate the virtual machine. The only pitfall in scenario 1 is the network traffic.

Conceptual models for designing information systems supporting the strategic analysis of technology environments

1 6 STRUCTURE OF THIS THESIS -Chapter I presents the motivations of this dissertation by illustrating two gaps in the current body of knowledge that are worth filling, describes the research problem addressed by this thesis and presents the research methodology used to achieve this goal. -Chapter 2 shows a review of the existing literature showing that environment analysis is a vital strategic task, that it shall be supported by adapted information systems, and that there is thus a need for developing a conceptual model of the environment that provides a reference framework for better integrating the various existing methods and a more formal definition of the various aspect to support the development of suitable tools. -Chapter 3 proposes a conceptual model that specifies the various enviromnental aspects that are relevant for strategic decision making, how they relate to each other, and ,defines them in a more formal way that is more suited for information systems development. -Chapter 4 is dedicated to the evaluation of the proposed model on the basis of its application to a concrete environment to evaluate its suitability to describe the current conditions and potential evolution of a real environment and get an idea of its usefulness. -Chapter 5 goes a step further by assembling a toolbox describing a set of methods that can be used to analyze the various environmental aspects put forward by the model and by providing more detailed specifications for a number of them to show how our model can be used to facilitate their implementation as software tools. -Chapter 6 describes a prototype of a strategic decision support tool that allow the analysis of some of the aspects of the environment that are not well supported by existing tools and namely to analyze the relationship between multiple actors and issues. The usefulness of this prototype is evaluated on the basis of its application to a concrete environment. -Chapter 7 finally concludes this thesis by making a summary of its various contributions and by proposing further interesting research directions.

Struggles for meaning and struggles for control: the diffusion of bandwagon technology in two institutional environments

In this thesis, I examine the diffusion process for a complex medical technology, the PET scanner, in two different health care systems, one of which is more market-oriented (Switzerland) and the other more centrally managed by a public agency (Quebec). The research draws on institutional and socio-political theories of the diffusion of innovations to examine how institutional contexts affect processes of diffusion. I find that diffusion proceeds more rapidly in Switzerland than in Quebec, but that processes in both jurisdictions are characterized by intense struggles among providers and between providers and public agencies. I show that the institutional environment influences these processes by determining the patterns of material resources and authority available to actors in their struggles to strategically control the technology, and by constituting the discursive resources or institutional logics on which actors may legitimately draw in their struggles to give meaning to the technology in line with their interests and values. This thesis illustrates how institutional structures and meanings manifest themselves in the context of specific decisions within an organizational field, and reveals the ways in which governance structures may be contested and realigned when they conflict with interests that are legitimized by dominant institutional logics. It is argued that this form of contestation and readjustment at the margins constitutes one mechanism by which institutional frameworks are tested, stretched and reproduced or redefined.

Biogeography and evolution of Amazonian triatomines (Heteroptera: Reduviidae): implications for Chagas disease surveillance in humid forest ecoregions

An ecological-evolutionary classification of Amazonian triatomines is proposed based on a revision of their main contemporary biogeographical patterns. Truly Amazonian triatomines include the Rhodniini, the Cavernicolini, and perhaps Eratyrus and some Bolboderini. The tribe Rhodniini comprises two major lineages (pictipes and robustus). The former gave rise to trans-Andean (pallescens) and Amazonian (pictipes) species groups, while the latter diversified within Amazonia (robustus group) and radiated to neighbouring ecoregions (Orinoco, Cerrado-Caatinga-Chaco, and Atlantic Forest). Three widely distributed Panstrongylus species probably occupied Amazonia secondarily, while a few Triatoma species include Amazonian populations that occur only in the fringes of the region. T. maculata probably represents a vicariant subset isolated from its parental lineage in the Caatinga-Cerrado system when moist forests closed a dry trans-Amazonian corridor. These diverse Amazonian triatomines display different degrees of synanthropism, defining a behavioural gradient from household invasion by adult triatomines to the stable colonisation of artificial structures. Anthropogenic ecological disturbance (driven by deforestation) is probably crucial in the onset of the process, but the fact that only a small fraction of species effectively colonises artificial environments suggests a role for evolution at the end of the gradient. Domestic infestation foci are restricted to drier subregions within Amazonia; thus, populations adapted to extremely humid rainforest microclimates may have limited chances of successfully colonising the slightly drier artificial microenvironments. These observations suggest several research avenues, from the use of climate data to map risk areas to the assessment of the synanthropic potential of individual vector species.

The ghost of social environments past: dominance relationships include current interactions and experience carried over from previous groups.

Dominance hierarchies pervade animal societies. Within a static social environment, in which group size and composition are unchanged, an individual's hierarchy rank results from intrinsic (e.g. body size) and extrinsic (e.g. previous experiences) factors. Little is known, however, about how dominance relationships are formed and maintained when group size and composition are dynamic. Using a fusion-fission protocol, we fused groups of previously isolated shore crabs (Carcinus maenas) into larger groups, and then restored groups to their original size and composition. Pre-fusion hierarchies formed independently of individuals' sizes, and were maintained within a static group via winner/loser effects. Post-fusion hierarchies differed from pre-fusion ones; losing fights during fusion led to a decline in an individual's rank between pre- and post-fusion conditions, while spending time being aggressive during fusion led to an improvement in rank. In post-fusion tanks, larger individuals achieved better ranks than smaller individuals. In conclusion, dominance hierarchies in crabs represent a complex combination of intrinsic and extrinsic factors, in which experiences from previous groups can carry over to affect current competitive interactions.