Técnicas de análise do perfil de execução e otimização de programas em química computacional

In this paper we review the basic techniques of performance analysis within the UNIX environment that are relevant in computational chemistry, with particular emphasis on the execution profile using the gprof tool. Two case studies (in ab initio and molecular dynamics calculations) are presented in order to illustrate how execution profiling can be used to effectively identify bottlenecks and to guide source code optimization. Using these profiling and optimization techniques it was possible to obtain significant speedups (of up to 30%) in both cases.

Development a distributed simulation environment on a cluster of workstations

Simulation has traditionally been used for analyzing the behavior of complex real world problems. Even though only some features of the problems are considered, simulation time tends to become quite high even for common simulation problems. Parallel and distributed simulation is a viable technique for accelerating the simulations. The success of parallel simulation depends heavily on the combination of the simulation application, algorithm and message population in the simulation is sufficient, no additional delay is caused by this environment. In this thesis a conservative, parallel simulation algorithm is applied to the simulation of a cellular network application in a distributed workstation environment. This thesis presents a distributed simulation environment, Diworse, which is based on the use of networked workstations. The distributed environment is considered especially hard for conservative simulation algorithms due to the high cost of communication. In this thesis, however, the distributed environment is shown to be a viable alternative if the amount of communication is kept reasonable. Novel ideas of multiple message simulation and channel reduction enable efficient use of this environment for the simulation of a cellular network application. The distribution of the simulation is based on a modification of the well known Chandy-Misra deadlock avoidance algorithm with null messages. The basic Chandy Misra algorithm is modified by using the null message cancellation and multiple message simulation techniques. The modifications reduce the amount of null messages and the time required for their execution, thus reducing the simulation time required. The null message cancellation technique reduces the processing time of null messages as the arriving null message cancels other non processed null messages. The multiple message simulation forms groups of messages as it simulates several messages before it releases the new created messages. If the message population in the simulation is suffiecient, no additional delay is caused by this operation A new technique for considering the simulation application is also presented. The performance is improved by establishing a neighborhood for the simulation elements. The neighborhood concept is based on a channel reduction technique, where the properties of the application exclusively determine which connections are necessary when a certain accuracy for simulation results is required. Distributed simulation is also analyzed in order to find out the effect of the different elements in the implemented simulation environment. This analysis is performed by using critical path analysis. Critical path analysis allows determination of a lower bound for the simulation time. In this thesis critical times are computed for sequential and parallel traces. The analysis based on sequential traces reveals the parallel properties of the application whereas the analysis based on parallel traces reveals the properties of the environment and the distribution.

Optimización del framework de paralelización de tareas COMPSs

El propósito de este trabajo es optimizar el sistema de gestión de workflows COMPSs caracterizando el comportamiento de diferentes dispositivos de memoria a nivel de consumo energético y tiempo de ejecución. Para llevar a cabo este propósito, se ha implementado un servicio de caché para COMPSs para conseguir que sea consciente de la jerarquía de memoria y se han realizado múltiples experimentos para caracterizar los dispositivos de memoria y las mejoras en el rendimiento.

Entrenamiento de la fuerza orientado a la mejora de la velocidad de golpeo en tenis

El golpeo de la bola a velocidades elevadas, es un factor determinante para el rendimiento en el tenis moderno. Durante los últimos 20 años se ha producido una gran evolución del juego y los cambios en el juego moderno se han traducido en el uso de poderosos servicios y golpes de fondo. Aunque la fuerza es una capacidad determinante desde la perspectiva de la condición física, ha habido poca investigación para fundamentar la eficacia de los programas de entrenamiento de fuerza para los jugadores de tenis. El objetivo de este estudio es realizar una revisión sobre los criterios básicos para dirigir correctamente el entrenamiento de la fuerza orientado a la mejora de la de la velocidad de golpeo de la pelota. Aunque las necesidades de fuerza dinámica máxima (FDM) en los golpeos son bajas, la literatura científica parece apuntar que unos adecuados niveles de FDM ejercen efectos positivos sobre el aumento de velocidad de golpeo en el tenis. La mejora y mantenimiento de esta manifestación de fuerza se busca a expensas de factores neurales. Los entrenamientos de fuerza útil deben utilizar medios que permitan ejecutar el gesto técnico, implicar las mismas cadenas musculares, rango de movimiento o velocidades de ejecución. En este sentido, se han propuesto la utilización de pelotas medicinales, mancuernas de peso ligero, gomas elásticas, máquinas multifuncionales de resistencia neumática o poleas.

Strategian toimeenpanokeinot muuttuvissa toimintaympäristöissä

Nykyinen strategia ajattelu perustuu filosofiaan, jossa yrityksen aineeton pääoma muuttuu aineelliseksi tulokseksi organisaatioiden resursseja, kyvykkyyksiä ja osaamista hyödyntämällä. Strategisissa tuloskorteissa oppimisen ja kasvun näkökulma kuvaa, miten ihmiset, teknologia ja organisaatioilmapiiri voivat toimia yhdessä strategian toimeenpanemiseksi. Oppimisen ja kasvun tulosten paraneminen ennakoi parannusta myös sisäisiin prosesseihin, asiakasnäkökulmaan ja taloudelliseen menestykseen. Työn teoriaosuudessa luotiin laaja katsaus eri strategiakoulukuntiin, keskittyen etenkin Mintzbergin konfiguraatio strategiakoulukunnan oppeihin. Tämän pohjalta tehtiin määritys strategia ajattelulle; strategiaprosessille ja strategialle muuttuvissa toimintaympäristöissä. Strategiaprosessin kriittiset alueet, sekä strategialähtöisen organisaation periaatteet huomioon ottaen, tehtiin kirjallisuuskartoitusta strategian toimeenpanokeinoista ja käytännön tutkimus niiden käytön yleisyydestä eri organisaatioissa. Tulosten mukaisesti monet keinot ovat aktiivisessa käytössä, mutta toisaalta on nähtävissä, että erilaiset yrityskulttuurit, organisaatioiden "elämäntilanteet" ja resurssien erilaisuudet tarjoavat erilaiset mahdollisuudet strategian toimeenpanoon ja organisaation osaamisen lisäämiseen. Nopeasti muuttuva toimintaympäristö korostaa joustavaa strategian ja sen toimeenpanon tarvetta. Osaamisen kehittäminen johtaa kasvuun; sen varmistamiseksi on löydettävä omalle organisaatioille sopivat keinot jatkuvaan oppimiseen, muutoskykyisyyden ja sitä kautta kilpailukyvyn saavuttamiseen ja ylläpitämiseen.

Logistisen tiedon hallita toimitusprojektissa

Distributed supply chains, tight delivery times and tailor made products are typical for international project business. This type of environment sets great challenges for logistics management. The scope of this work was to study logistics and information management in delivery projects. The logistic information of delivery project is divided into four categories: The information used to plan, execute and follow up the material flow and the information directly embedded into material flow. On the practical study the operations of the target company are dived into main processes supporting project execution. Logistic information is studied by modelling information flows between the processes. The aim was to identify the information crucial for project materials management and describe the flow of information between the processes. Results of the study show that the information related to execution of material flow is usually emphasized when it comes to operations and tools for data management. The traditional system tools poorly support the planning of material flow in project environment. In addition the significance of clearly defined and documented practices is highlighted.

Supply Risk Management in Pharmaceutical

Fast development in the operating environment and fierce competition have driven companies to pursue efficiency and success through lean and global supply chains. At the same time overall uncertainty has increased in the business environment and supply chains have become a priority in risk management since their vulnerability may endanger business continuity. Although risk management should start at procurement strategy development phase, proactive contingency planning is also essential because it enables correct reaction and fast changes in process execution in the case of risk realization. This thesis is a case study conducted in the pharmaceutical industry where purchasing and materials management organizations face a number of challenges and limitations that have to be considered in supply risk management. The goal of the study was to discuss the operating environment, and identify and analyze supply risks and potential risk management practices. The study was concluded with suggestions for purchasing strategy development that take risk management considerations into account. This copy is the public version of the thesis.

RTOS Framework for Real-Time Control System

This thesis is done as a complementary part for the active magnet bearing (AMB) control software development project in Lappeenranta University of Technology. The main focus of the thesis is to examine an idea of a real-time operating system (RTOS) framework that operates in a dedicated digital signal processor (DSP) environment. General use real-time operating systems do not necessarily provide sufficient platform for periodic control algorithm utilisation. In addition, application program interfaces found in real-time operating systems are commonly non-existent or provided as chip-support libraries, thus hindering platform independent software development. Hence, two divergent real-time operating systems and additional periodic extension software with the framework design are examined to find solutions for the research problems. The research is discharged by; tracing the selected real-time operating system, formulating requirements for the system, and designing the real-time operating system framework (OSFW). The OSFW is formed by programming the framework and conjoining the outcome with the RTOS and the periodic extension. The system is tested and functionality of the software is evaluated in theoretical context of the Rate Monotonic Scheduling (RMS) theory. The performance of the OSFW and substance of the approach are discussed in contrast to the research theme. The findings of the thesis demonstrates that the forged real-time operating system framework is a viable groundwork solution for periodic control applications.

Organisaation toimintamallin muutoksen toteuttaminen

Työn tavoitteena oli selvittää mitä erityspiirteitä esiintyy siirryttäessä kompetenssipohjaiseen organisaatiorakenteeseen ja toimintaan sekä kuvata muutoksen toteutusprosessi. Tutkimus pitää sisällään kaksi keskeisintä ja tärkeää käsitettä: osaamisrakenteen muutos ja sen johtaminen. Empiirinen osa on toteutettu kyselylomakkeen avulla, joka lähetettiin valituille Case-yrityksen operatiivisesta johtamisesta vastuussa oleville esimiehille. Organisaation muutoksen toteuttaminen on erittäin vaativa toimenpide, joka vaikuttaa organisaation jokaiseen henkilöön ja heidän päivittäisiin työtehtäviinsä. Muutoksen toteuttaminen vaatii paljon aikaa, mutta ennen kaikkea kärsivällisyyttä. Mitä isommasta organisaatiosta on kysymys, sitä vaikeampaa toteuttaminen on. Muutokseen vaikuttavat oman henkilöstön lisäksi organisaation ulkoiset tekijät, kuten asiakkaat, markkinat sekä erilaiset osaamiseen ja teknologiaan liittyvät uudenlaiset osaamisvaatimukset. Tärkein tekijä muutoksen onnistumisen kannalta on tiedostaa koko organisaation tasolla, miksi muutokseen lähdetään ja mitkä ovat muutoksen tavoitteet. Tavoitellaanko muutoksella pientä hienosäätöä organisaation toiminnassa vai onko taustalla kokonaan uuden toimintamallin käyttöönotto uudenlaisia strategisia linjauksia myöten.

Groupware and Workflow Tools - A Case study of SAP Business Workflow Supporting System Integration in a Global Telecommunication Company

Workflow management systems aim at the controlled execution of complex application processes in distributed and heterogeneous environments. These systems will shape the structure of information systems in business and non-business environments. E business and system integration is a fertile soil for WF and groupware tools. This thesis aims to study WF and groupware tools in order to gather in house knowledge of WF to better utilize WF solutions in future, and to focus on SAP Business Workflow in order to find a global solution for Application Link Enabling support for system integration. Piloting this solution in Nokia collects the experience of SAP R/3 WF tool for other development projects in future. The literary part of this study will guide to the world of business process automation providing a general description of the history, use and potentials of WF & groupware software. The empirical part of this study begins with the background of the case study describing the IT environment initiating the case by introducing SAP R/3 in Nokia, the communication technique in use and WF tool. Case study is focused in one solution with SAP Business Workflow. This study provides a concept to monitor communication between ERP systems and to increase the quality of system integration. Case study describes a way create support model for ALE/EDI interfaces. Support model includes monitoring organization and the workflow processes to solve the most common IDoc related errors.

Conseqüências da análise incorreta de experimentos blocados

Errors are always present in experimental measurements so, it is important to identify them and understand how they affect the results of experiments. Statistics suggest that the execution of experiments should follow random order, but unfortunately the complete randomization of experiments is not always viable for practical reasons. One possible simplification is blocked experiments within which the levels of certain factors are maintained fixed while the levels of others are randomized. However this has a cost. Although the experimental part is simplified, the statistical analysis becomes more complex.

Projecte de legalització d'una activitat dedicada a l'explotació ramadera i a la formatgeria artesanal

La integració en una mateixa activitat d'una explotació ramadera ecològica basada en el bestiar cabrú de llet i d'una formatgeria artesanal basada en varietats autòctones de formatge de cabra, permet ocupar un nínxol de mercat encara poc explotat actualment a Catalunya. D'igual manera, la dificultat que tenen actualment molts dels formatgers artesans del país per trobar llet de cabra en quantitats suficients i amb unes mínimes garanties higiènico-sanitàries dificulten l'avanç d'un sector amb molt bones perspectives de futur com és el de la formatgeria artesanal i justifica la necessitat de crear noves explotacions (o reconvertir-ne de ja existents) orientant-les de ple vers l'aprofitament lleter del bestiar cabrú, que és actualment molt reduït en l'àmbit Català. A més d'això, les actuals exigències en el camp del benestar animal així com en el camp de la qualitat i de la seguretat alimentaria, exigeixen a les explotacions ramaderes i a les indústries alimentàries el compliment d'una sèrie de requisits, tan de disseny dels locals i de les instal•lacions, com de control de les activitats i dels productes elaborats, que garanteixin en tot moment la seva correcte gestió i funcionament en aquestes matèries. L'objectiu d'aquest projecte, doncs, és la legalització d'una activitat, que anomenarem “Mas Peirot, S.L.”, dedicada a l'explotació ramadera ecològica de bestiar cabrú de llet i a la formatgeria artesanal de formatge de cabra. És important mencionar que tot i tractar-se d'un projecte de legalització d'una activitat,, també s'hi han contemplat aspectes i detalls relacionats amb l'execució de la mateixa, al tractar-se d'unes obres d'una certa complexitat i considerant que així es tracten amb més detall i rigorositat les actuacions projectades. En concret, en aquest projecte es planifiquen les operacions de rehabilitació de dues naus ramaderes actualment en desús, per tal que puguin destinar-se a l'explotació ramadera de bestiar cabrú i a la formatgeria artesanal, projectant-se així mateix totes les instal•lacions necessàries per tal que a les mencionades naus s'hi puguin desenvolupar les activitats citades. Com a conclusions més importants d'aquest projecte podem dir que amb un cens de 100 caps de bestiar cabrú és possible obtenir una producció mitjana de llet de 32.500 litres anuals, que es corresponen a un volum total de 3.823 quilograms de formatge a l'any (de les tipologies Formatge Garrotxa i Formatge de cabra amb oli, ambdues varietats tradicionals catalanes) obtenint un benefici de 21.389,47 Euros/any durant els primers 15 anys i un benefici de 33.386,39 Euros/any a partir del 16è any, cosa que permetrà recuperar la inversió inicial de 172.716,76 Euros que valen les naus i instal•lacions projectades, en un termini de 8 anys i permetrà, com s'ha dit, ocupar un nínxol de mercat encara poc explotat per la indústria agroalimentària a Catalunya.

Moottoripyörän rungon muuntelun valvontakriteerit muutoskatsastuksessa

Muutoskatsastusta koskeva lainsäädäntö aiheuttaa tulkintavaikeuksia ja rajoitteita moottoripyöräharrastajille ja alan toimijoille. Nykyinen asetus edellyttää tarvittaessa asiantuntijaselvitystä rakennemuutoksen lujuudesta ja hitsaustyöstä. Moottoripyörän geometria on laissa rajattu akselivälin ja emäputken kulman osalta. Moottoripyörien runkoja valmistetaan hitsaamalla seostamattomista teräksistä ja lämpökäsiteltävistä alumiini- ja terässeoksista. Runkojen muuntelu suoritetaan myös yleisesti hitsaamalla. Turvallisuuden kannalta tärkeiltä hitsausliitoksilta vaaditaan hyvää laatua, joka saavutetaan oikeilla hitsausparametreilla ja -suorituksella. Vaatimukset seostamattomalle teräkselle voidaan täyttää pätevöityneen hitsaajan toimesta. Lämpökäsiteltävät seokset vaativat lisäksi jälkilämpökäsittelyn, mikä edelleen vaikeuttaa runkojen hitsausta. Hitsien laadun merkitystä moottoripyörän rungossa tutkittiin soveltamalla rajoitetun vahingon periaatetta. Vauriotapauksena mallinnettiin satunnaisen rungon hitsausliitoksen murtuminen. Eri kuormitustilanteissa elementtimenetelmää hyödyntäen todettiin chopper-tyyppisten moottoripyörien runkojen olevan osittain vauriosietoisia ja havaittiin kriittiset hitsausliitokset emä- ja vaakaputken alueilla. Moottoripyörien runkojen kriittisiä hitsausliitoksia tarkasteltiin väsymisen kannalta. Soveltamalla tehollista lovijännitystä, vertailtiin emäputken hitsausliitosten väsymiskestävyyttä oletetulla kuormituksella. Tulosten perusteella muunneltu moottoripyörän runko voi olla alkuperäisrunkoa kestävämpi tai heikompi. Moottoripyörän akseliväli tai emäputken kulma eivät määrää kestävyyttä, vaan rakenteen yksityiskohtainen suunnittelu. Kriittisten liitosten väsymiskestävyyksissä havaittiin merkittäviä eroja eri mallien välillä.

Differential Regulation of c-FLIP Isoforms Through Post-translational Modifications

Cells are constantly responding to signals from the surrounding tissues and the environment. To dispose of infected and potentially dangerous cells, to ensure the optimal execution of developmental processes and to maintain tissue homeostasis, a multicellular organism needs to tightly control both the number and the quality of its cells. Apoptosis is a form of active cellular self-destruction that enables an organism to regulate its cell number by deleting damaged or potentially dangerous cells. Apoptosis can be induced by death ligands, which bind to death receptors on the cell surface. Ligation of the receptors leads to the formation of an intracellular death inducing signaling complex (DISC). One of the DISC components is caspase-8, a protease that triggers the caspase cascade and is thereby a key initiator of programmed cell death. The activation of caspase-8 is controlled by the cellular FLICE-inhibitory proteins (c-FLIPs). Consequently, sensitivity towards receptor-mediated apoptosis is determined by the amount of c-FLIP, and the c-FLIP levels are actively regulated for example during erythroid differentiation of K562 erythroleukemia cells and by hyperthermia in Jurkat leukemia cells. The aim of my thesis was to investigate how c-FLIP is regulated during these processes. We found that c-FLIP isoforms are short-lived proteins, although c-FLIPS had an even shorter half-life than c-FLIPL. In both experimental models, increased death receptor sensitivity correlated with induced ubiquitylation and consequent proteasomal degradation of c-FLIP. Furthermore, we elucidated how phosphorylation regulates the biological functions and the turnover of c-FLIP, thereby contributing to death receptor sensitivity. We mapped the first phosphorylation sites on c-FLIP and dissected how their phosphorylation affects c-FLIP. Moreover, we demonstrated that phosphorylation of serine 193, a phosphorylated residue common to all c-FLIPs, is primarily mediated by the classical PKC. Furthermore, we discovered a novel connection between the phosphorylation and ubiquitylation of c-FLIP: phosphorylation of S193 protects c-FLIP from ubiquitylation. Surprisingly, although all c-FLIP isoforms are phosphorylated on this conserved residue, the biological outcome is different for the long and short isoforms, since S193 specifically prolongs the half-lives of the short c-FLIP isoforms, but not c-FLIPL. To summarize, we show that c-FLIP proteins are modified by ubiquitylation and phosphorylation, and that the biological outcomes of these modifications are isoform-specifically determined.

Determinação potenciométrica da concentração micelar crítica de surfactantes: uma nova aplicação metodológica no ensino de Química

The participation of the students in the planning, execution and discussion of experimental results is important for the valuation of the role of them in the construction of the chemical knowledge implicited in the approach between education and research. This work relates either the construction of selective membrane electrodes for surfactants and its application in the potenciometric determination of the critical micellar concentration of the sodium dodecyl sulfate (SDS) and dodecyltrimethylammonium bromide (DTAB) surfactants. In adition it´s possible to discuss the potenciometric results in matching with the data valued for the tensiometric and condutimetric traditionally used in the physical-chemistry lessons.