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.

Addressing Sea Surface Salinity retrieval at different spatial resolution. Feasibility study using OCCAM data within SEPS simulator and L2 processor tools

Projecte de recerca elaborat a partir d’una estada a la National Oceanography Centre of Southampton (NOCS), Gran Bretanya, entre maig i juliol del 2006. La possibilitat d’obtenir una estimació precissa de la salinitat marina (SSS) és important per a investigar i predir l’extensió del fenòmen del canvi climàtic. La missió Soil Moisture and Ocean Salinity (SMOS) va ser seleccionada per l’Agència Espacial Europea (ESA) per a obtenir mapes de salinitat de la superfície marina a escala global i amb un temps de revisita petit. Abans del llençament de SMOS es preveu l’anàlisi de la variabilitat horitzontal de la SSS i del potencial de les dades recuperades a partir de mesures de SMOS per a reproduir comportaments oceanogràfics coneguts. L’objectiu de tot plegat és emplenar el buit existent entre les fonts de dades d’entrada/auxiliars fiables i les eines desenvolupades per a simular i processar les dades adquirides segons la configuració de SMOS. El SMOS End-to-end Performance Simulator (SEPS) és un simulador adhoc desenvolupat per la Universitat Politècnica de Catalunya (UPC) per a generar dades segons la configuració de SMOS. Es va utilitzar dades d’entrada a SEPS procedents del projecte Ocean Circulation and Climate Advanced Modeling (OCCAM), utilitzat al NOCS, a diferents resolucions espacials. Modificant SEPS per a poder fer servir com a entrada les dades OCCAM es van obtenir dades de temperatura de brillantor simulades durant un mes amb diferents observacions ascendents que cobrien la zona seleccionada. Les tasques realitzades durant l’estada a NOCS tenien la finalitat de proporcionar una tècnica fiable per a realitzar la calibració externa i per tant cancel•lar el bias, una metodologia per a promitjar temporalment les diferents adquisicions durant les observacions ascendents, i determinar la millor configuració de la funció de cost abans d’explotar i investigar les posibiltats de les dades SEPS/OCCAM per a derivar la SSS recuperada amb patrons d’alta resolució.

An approach for linking score and audio recordings in Makam music of Turkey

The main information sources to study a particular piece of music are symbolic scores and audio recordings. These are complementary representations of the piece and it isvery useful to have a proper linking between the two of the musically meaningful events. For the case of makam music of Turkey, linking the available scores with the correspondingaudio recordings requires taking the specificities of this music into account, such as the particular tunings, the extensive usage of non-notated expressive elements, and the way in which the performer repeats fragmentsof the score. Moreover, for most of the pieces of the classical repertoire, there is no score written by the original composer. In this paper, we propose a methodology to pair sections of a score to the corresponding fragments of audio recording performances. The pitch information obtained from both sources is used as the common representationto be paired. From an audio recording, fundamental frequency estimation and tuning analysis is done to compute a pitch contour. From the corresponding score, symbolic note names and durations are converted to a syntheticpitch contour. Then, a linking operation is performed between these pitch contours in order to find the best correspondences.The method is tested on a dataset of 11 compositions spanning 44 audio recordings, which are mostly monophonic. An F3-score of 82% and 89% are obtained with automatic and semi-automatic karar detection respectively,showing that the methodology may give us a needed tool for further computational tasks such as form analysis, audio-score alignment and makam recognition.

Sintonización dinámica de aplicaciones MPI

En la actualidad, la computación de altas prestaciones está siendo utilizada en multitud de campos científicos donde los distintos problemas estudiados se resuelven mediante aplicaciones paralelas/distribuidas. Estas aplicaciones requieren gran capacidad de cómputo, bien sea por la complejidad de los problemas o por la necesidad de solventar situaciones en tiempo real. Por lo tanto se debe aprovechar los recursos y altas capacidades computacionales de los sistemas paralelos en los que se ejecutan estas aplicaciones con el fin de obtener un buen rendimiento. Sin embargo, lograr este rendimiento en una aplicación ejecutándose en un sistema es una dura tarea que requiere un alto grado de experiencia, especialmente cuando se trata de aplicaciones que presentan un comportamiento dinámico o cuando se usan sistemas heterogéneos. En estos casos actualmente se plantea realizar una mejora de rendimiento automática y dinámica de las aplicaciones como mejor enfoque para el análisis del rendimiento. El presente trabajo de investigación se sitúa dentro de este ámbito de estudio y su objetivo principal es sintonizar dinámicamente mediante MATE (Monitoring, Analysis and Tuning Environment) una aplicación MPI empleada en computación de altas prestaciones que siga un paradigma Master/Worker. Las técnicas de sintonización integradas en MATE han sido desarrolladas a partir del estudio de un modelo de rendimiento que refleja los cuellos de botella propios de aplicaciones situadas bajo un paradigma Master/Worker: balanceo de carga y número de workers. La ejecución de la aplicación elegida bajo el control dinámico de MATE y de la estrategia de sintonización implementada ha permitido observar la adaptación del comportamiento de dicha aplicación a las condiciones actuales del sistema donde se ejecuta, obteniendo así una mejora de su rendimiento.

Aplicación de la ingeniería software sobre la herramienta MATE Analyzer

MATE (Monitoring, Analysis and Tuning Environment) es un proyecto que surge en 2004 como tesis doctoral de Anna Sikora con el propósito de investigar la mejora de rendimiento de aplicaciones paralelas a través de la modificación dinámica. Nuestro proyecto supone un paso adelante en cuestiones de calidad de software y pretende dotar al proyecto MATE de una base de desarrollo sólida de cara a futuras lineas de trabajo. Para ello se hace frente a la problemática desde tres perspectivas: la creación de una metodología de desarrollo (y su aplicación sobre el proyecto existente), la implantación de un entorno de desarrollo de soporte y el desarrollo de nuevas características para favorecer la portabilidad y la usabilidad, entre otros aspectos.

Tuning synchronization of integrate-and-fire oscillators through mobility

We analyze the emergence of synchronization in a population of moving integrate-and-fire oscillators. Oscillators, while moving on a plane, interact with their nearest neighbor upon firing time. We discover a nonmonotonic dependence of the synchronization time on the velocity of the agents. Moreover, we find that mechanisms that drive synchronization are different for different dynamical regimes. We report the extreme situation where an interplay between the time scales involved in the dynamical processes completely inhibits the achievement of a coherent state. We also provide estimators for the transitions between the different regimes.

Catalytic tuning of phosphinoethane ligand. An improved catalyst for hydrocarbon

Report for the scientific sojourn carried out at the Department of Chemistry University of North Texas (USA) from September until November 2006. It includes the performance of two computational chemistry studies: an experimental and computational study toward the intra- and intermolecular hydroarylation of isonitriles and the development of an improved catalyst for hydrocarbon functionalization.

Female stereotypes in household appliances advertising and their social role in Spain: the perpetuation of a no- longer-existing female condition

The following dissertation proposes a qualitative approach on the matter ofadvertising, society and construction of identity, based on the effect of householdappliances commercials in constructing female identity of Spanish women today.Conclusions will be drawn based on a juxtaposition of social background andadvertising content and on how Spanish women of today perceive the evolution offemale imagery depicted in advertisements. The aim is to demonstrate how muchcommercials mirrors society and how far it reinforces paradigms no longer existing

ILS-ESP An efficient, simple, and parameter-free algorithm for solving the permutation flow-shop problem

From a managerial point of view, the more effcient, simple, and parameter-free (ESP) an algorithm is, the more likely it will be used in practice for solving real-life problems. Following this principle, an ESP algorithm for solving the Permutation Flowshop Sequencing Problem (PFSP) is proposed in this article. Using an Iterated Local Search (ILS) framework, the so-called ILS-ESP algorithm is able to compete in performance with other well-known ILS-based approaches, which are considered among the most effcient algorithms for the PFSP. However, while other similar approaches still employ several parameters that can affect their performance if not properly chosen, our algorithm does not require any particular fine-tuning process since it uses basic "common sense" rules for the local search, perturbation, and acceptance criterion stages of the ILS metaheuristic. Our approach defines a new operator for the ILS perturbation process, a new acceptance criterion based on extremely simple and transparent rules, and a biased randomization process of the initial solution to randomly generate different alternative initial solutions of similar quality -which is attained by applying a biased randomization to a classical PFSP heuristic. This diversification of the initial solution aims at avoiding poorly designed starting points and, thus, allows the methodology to take advantage of current trends in parallel and distributed computing. A set of extensive tests, based on literature benchmarks, has been carried out in order to validate our algorithm and compare it against other approaches. These tests show that our parameter-free algorithm is able to compete with state-of-the-art metaheuristics for the PFSP. Also, the experiments show that, when using parallel computing, it is possible to improve the top ILS-based metaheuristic by just incorporating to it our biased randomization process with a high-quality pseudo-random number generator.

Variable Kernel estimates: On the impossibility of tuning the parameters

For the standard kernel density estimate, it is known that one can tune the bandwidth such that the expected L1 error is within a constant factor of the optimal L1 error (obtained when one is allowed to choose the bandwidth with knowledge of the density). In this paper, we pose the same problem for variable bandwidth kernel estimates where the bandwidths are allowed to depend upon the location. We show in particular that for positive kernels on the real line, for any data-based bandwidth, there exists a densityfor which the ratio of expected L1 error over optimal L1 error tends to infinity. Thus, the problem of tuning the variable bandwidth in an optimal manner is ``too hard''. Moreover, from the class of counterexamples exhibited in the paper, it appears thatplacing conditions on the densities (monotonicity, convexity, smoothness) does not help.

Trade, migration and regional unemployment

We formulate a dynamic core-periphery model with frictions in the job matching process to study the interplay between trade costs, migration and regional unemploymentin the short- and long-run. We find that the spatial distribution of unemployment mirrors (inversely) the distribution of economic activities. Further, we highlight a contrast between the short-run and the long-run effects of trade-induced migration on regional unemployment. In particular, an inßow of immigrants from the periphery into the core reduces the unemployment gap in the short-run, but exacerbates unemployment disparities in the long-run.

Fine-Tuning Translation Kinetics Selection as the Driving Force of Codon Usage Bias in the Hepatitis A Virus Capsid

Hepatitis A virus (HAV), the prototype of genus Hepatovirus, has several unique biological characteristics that distinguish it from other members of the Picornaviridae family. Among these, the need for an intact eIF4G factor for the initiation of translation results in an inability to shut down host protein synthesis by a mechanism similar to that of other picornaviruses. Consequently, HAV must inefficiently compete for the cellular translational machinery and this may explain its poor growth in cell culture. In this context of virus/cell competition, HAV has strategically adopted a naturally highly deoptimized codon usage with respect to that of its cellular host. With the aim to optimize its codon usage the virus was adapted to propagate in cells with impaired protein synthesis, in order to make tRNA pools more available for the virus. A significant loss of fitness was the immediate response to the adaptation process that was, however, later on recovered and more associated to a re-deoptimization rather than to an optimization of the codon usage specifically in the capsid coding region. These results exclude translation selection and instead suggest fine-tuning translation kinetics selection as the underlying mechanism of the codon usage bias in this specific genome region. Additionally, the results provide clear evidence of the Red Queen dynamics of evolution since the virus has very much evolved to re-adapt its codon usage to the environmental cellular changing conditions in order to recover the original fitness.

A new and simple variable-angle accessory for infrared specular reflectance

A simple, low-cost accessory (patent pending) with only two flat mirrors and a new variable-angle mechanism has been developed for infrared specular reflectance measurements. The system allows the angles of incidence to be varied continuously from 15° (near normal incidence) to 85° (near grazing angle) without losing the alignment of the accessory. The reflectivity of boron nitride thin films deposited on metallic substrates has been measured at different angles of incidence to demonstrate the utility of this accessory.

Tuning clustering in random networks with arbitrary degree distributions

We present a generator of random networks where both the degree-dependent clustering coefficient and the degree distribution are tunable. Following the same philosophy as in the configuration model, the degree distribution and the clustering coefficient for each class of nodes of degree k are fixed ad hoc and a priori. The algorithm generates corresponding topologies by applying first a closure of triangles and second the classical closure of remaining free stubs. The procedure unveils an universal relation among clustering and degree-degree correlations for all networks, where the level of assortativity establishes an upper limit to the level of clustering. Maximum assortativity ensures no restriction on the decay of the clustering coefficient whereas disassortativity sets a stronger constraint on its behavior. Correlation measures in real networks are seen to observe this structural bound.

Fine-Tuning Translation Kinetics Selection as the Driving Force of Codon Usage Bias in the Hepatitis A Virus Capsid

Hepatitis A virus (HAV), the prototype of genus Hepatovirus, has several unique biological characteristics that distinguish it from other members of the Picornaviridae family. Among these, the need for an intact eIF4G factor for the initiation of translation results in an inability to shut down host protein synthesis by a mechanism similar to that of other picornaviruses. Consequently, HAV must inefficiently compete for the cellular translational machinery and this may explain its poor growth in cell culture. In this context of virus/cell competition, HAV has strategically adopted a naturally highly deoptimized codon usage with respect to that of its cellular host. With the aim to optimize its codon usage the virus was adapted to propagate in cells with impaired protein synthesis, in order to make tRNA pools more available for the virus. A significant loss of fitness was the immediate response to the adaptation process that was, however, later on recovered and more associated to a re-deoptimization rather than to an optimization of the codon usage specifically in the capsid coding region. These results exclude translation selection and instead suggest fine-tuning translation kinetics selection as the underlying mechanism of the codon usage bias in this specific genome region. Additionally, the results provide clear evidence of the Red Queen dynamics of evolution since the virus has very much evolved to re-adapt its codon usage to the environmental cellular changing conditions in order to recover the original fitness.