Data-parallel computation in parallel and distributed environments

The past few decades have seen a considerable increase in the number of parallel and distributed systems. With the development of more complex applications, the need for more powerful systems has emerged and various parallel and distributed environments have been designed and implemented. Each of the environments, including hardware and software, has unique strengths and weaknesses. There is no single parallel environment that can be identified as the best environment for all applications with respect to hardware and software properties. The main goal of this thesis is to provide a novel way of performing data-parallel computation in parallel and distributed environments by utilizing the best characteristics of difference aspects of parallel computing. For the purpose of this thesis, three aspects of parallel computing were identified and studied. First, three parallel environments (shared memory, distributed memory, and a network of workstations) are evaluated to quantify theirsuitability for different parallel applications. Due to the parallel and distributed nature of the environments, networks connecting the processors in these environments were investigated with respect to their performance characteristics. Second, scheduling algorithms are studied in order to make them more efficient and effective. A concept of application-specific information scheduling is introduced. The application- specific information is data about the workload extractedfrom an application, which is provided to a scheduling algorithm. Three scheduling algorithms are enhanced to utilize the application-specific information to further refine their scheduling properties. A more accurate description of the workload is especially important in cases where the workunits are heterogeneous and the parallel environment is heterogeneous and/or non-dedicated. The results obtained show that the additional information regarding the workload has a positive impact on the performance of applications. Third, a programming paradigm for networks of symmetric multiprocessor (SMP) workstations is introduced. The MPIT programming paradigm incorporates the Message Passing Interface (MPI) with threads to provide a methodology to write parallel applications that efficiently utilize the available resources and minimize the overhead. The MPIT allows for communication and computation to overlap by deploying a dedicated thread for communication. Furthermore, the programming paradigm implements an application-specific scheduling algorithm. The scheduling algorithm is executed by the communication thread. Thus, the scheduling does not affect the execution of the parallel application. Performance results achieved from the MPIT show that considerable improvements over conventional MPI applications are achieved.

Introducing massively parallel computers into operational weather forecasting

Numerical weather prediction and climate simulation have been among the computationally most demanding applications of high performance computing eversince they were started in the 1950's. Since the 1980's, the most powerful computers have featured an ever larger number of processors. By the early 2000's, this number is often several thousand. An operational weather model must use all these processors in a highly coordinated fashion. The critical resource in running such models is not computation, but the amount of necessary communication between the processors. The communication capacity of parallel computers often fallsfar short of their computational power. The articles in this thesis cover fourteen years of research into how to harness thousands of processors on a single weather forecast or climate simulation, so that the application can benefit as much as possible from the power of parallel high performance computers. The resultsattained in these articles have already been widely applied, so that currently most of the organizations that carry out global weather forecasting or climate simulation anywhere in the world use methods introduced in them. Some further studies extend parallelization opportunities into other parts of the weather forecasting environment, in particular to data assimilation of satellite observations.

On sliding mode control ofhydraulic servo systems and a manipulator

The aim of the study is to developa novel robust controller based on sliding mode control technique for the hydraulic servo system with flexible load and for a flexible manipulator with the lift and jib hydraulic actuators. For the purpose of general control design, a dynamic model is derived describing the principle physical behavior for both the hydraulic servo system and the flexible hydraulic manipulator. The mechanism of hydraulic servo systems is described by basic mathematical equations of fluid powersystems and the dynamics of flexible manipulator is modeled by the assumed modemethod. The controller is constructed so as to track desired trajectories in the presence of model imprecision. Experimental and simulation results demonstratethat sliding mode control has benefits which can be used to guarantee stabilityin uncertain systems and improve the system performance and load tolerance.

"Patron-driven acquisitions": la biblioteca propone y el lector dispone

Reseña de: Esposito, Joseph J.; Walker, Kizer; Ehling, Terry. PDA and the university press. A report prepared for The Andrew W. Mellon Foundation. [Baltimore, Md]: The Johns Hopkins University Press; [Ithaca, N.Y.]: Cornell University Library, Sept. 26th 2012. 65 p. Documento de trabajo disponible en línea en: . [Consulta: 10 de mayo de 2013].

What to consider for applying backfilling on non-dedicated environments

The resource utilization level in open laboratories of several universities has been shown to be very low. Our aim is to take advantage of those idle resources for parallel computation without disturbing the local load. In order to provide a system that lets us execute parallel applications in such a non-dedicated cluster, we use an integral scheduling system that considers both Space and Time sharing concerns. For dealing with the Time Sharing (TS) aspect, we use a technique based on the communication-driven coscheduling principle. This kind of TS system has some implications on the Space Sharing (SS) system, that force us to modify the way job scheduling is traditionally done. In this paper, we analyze the relation between the TS and the SS systems in a non-dedicated cluster. As a consequence of this analysis, we propose a new technique, termed 3DBackfilling. This proposal implements the well known SS technique of backfilling, but applied to an environment with a MultiProgramming Level (MPL) of the parallel applications that is greater than one. Besides, 3DBackfilling considers the requirements of the local workload running on each node. Our proposal was evaluated in a PVM/MPI Linux cluster, and it was compared with several more traditional SS policies applied to non-dedicated environments.

Spatially varying selection shapes life history clines among populations of Drosophila melanogaster from sub-Saharan Africa.

Clines in life history traits, presumably driven by spatially varying selection, are widespread. Major latitudinal clines have been observed, for example, in Drosophila melanogaster, an ancestrally tropical insect from Africa that has colonized temperate habitats on multiple continents. Yet, how geographic factors other than latitude, such as altitude or longitude, affect life history in this species remains poorly understood. Moreover, most previous work has been performed on derived European, American and Australian populations, but whether life history also varies predictably with geography in the ancestral Afro-tropical range has not been investigated systematically. Here, we have examined life history variation among populations of D. melanogaster from sub-Saharan Africa. Viability and reproductive diapause did not vary with geography, but body size increased with altitude, latitude and longitude. Early fecundity covaried positively with altitude and latitude, whereas lifespan showed the opposite trend. Examination of genetic variance-covariance matrices revealed geographic differentiation also in trade-off structure, and QST -FST analysis showed that life history differentiation among populations is likely shaped by selection. Together, our results suggest that geographic and/or climatic factors drive adaptive phenotypic differentiation among ancestral African populations and confirm the widely held notion that latitude and altitude represent parallel gradients.

Reexposure and advection of C-14-depleted organic carbon from old deposits at the upper continental slope

Outcrops of old strata at the shelf edge resulting from erosive gravity-driven flows have been globally described on continental margins. The reexposure of old strata allows for the reintroduction of aged organic carbon (OC), sequestered in marine sediments for thousands of years, into the modern carbon cycle. This pool of reworked material represents an additional source of C-14-depleted organic carbon supplied to the ocean, in parallel with the weathering of fossil organic carbon delivered by rivers from land. To understand the dynamics and implications of this reexposure at the shelf edge, a biogeochemical study was carried out in the Gulf of Lions (Mediterranean Sea) where erosive processes, driven by shelf dense water cascading, are currently shaping the seafloor at the canyon heads. Mooring lines equipped with sediment traps and current meters were deployed during the cascading season in the southwestern canyon heads, whereas sediment cores were collected along the sediment dispersal system from the prodelta regions down to the canyon heads. Evidence from grain-size, X-radiographs and Pb-210 activity indicate the presence in the upper slope of a shelly-coarse surface stratum overlying a consolidated deposit. This erosive discontinuity was interpreted as being a result of dense water cascading that is able to generate sufficient shear stress at the canyon heads to mobilize the coarse surface layer, eroding the basal strata. As a result, a pool of aged organic carbon (Delta C-14 = -944.5 +/- 24.7%; mean age 23,650 +/- 3,321 ybp) outcrops at the modern seafloor and is reexposed to the contemporary carbon cycle. This basal deposit was found to have relatively high terrigenous organic carbon (lignin = 1.48 +/- 0.14 mg/100 mg OC), suggesting that this material was deposited during the last low sea-level stand. A few sediment trap samples showed anomalously depleted radiocarbon concentrations (Delta C-14 = -704.4 +/- 62.5%) relative to inner shelf (Delta C-14 = -293.4 +/- 134.0%), mid-shelf (Delta C-14 = -366.6 +/- 51.1%), and outer shelf (Delta C-14 = -384 +/- 47.8%) surface sediments. Therefore, although the major source of particulate material during the cascading season is resuspended shelf deposits, there is evidence that this aged pool of organic carbon can be eroded and laterally advected downslope.

Spontaneous Emergence of Chirality in the Limited Enantioselectivity Model: Autocatalytic Cycle Driven by an External Reagent

The emergence of chirality in enantioselective autocatalysis for compounds unable to transform according to the Frank-like reaction network is discussed with respect to the controversial limited enantioselectivity (LES) model composed of coupled enantioselective and non-enantioselective autocatalyses. The LES model cannot lead to spontaneous mirror symmetry breaking (SMSB) either in closed systems with a homogeneous temperature distribution or in closed systems with a stationary non-uniform temperature distribution. However, simulations of chemical kinetics in a two-compartment model demonstrate that SMSB may occur if both autocatalytic reactions are spatially separated at different temperatures in different compartments but coupled under the action of a continuous internal flow. In such conditions, the system can evolve, for certain reaction and system parameters, toward a chiral stationary state; that is, the system is able to reach a bifurcation point leading to SMSB. Numerical simulations in which reasonable chemical parameters have been used suggest that an adequate scenario for such a SMSB would be that of abyssal hydrothermal vents, by virtue of the typical temperature gradients found there and the role of inorganic solids mediating chemical reactions in an enzyme-like role.

Assessment of critical competences required in managing end-user driven businesses in a global forest products compa

Työn pääasiallisena tavoitteena on selvittää ydinosaamista, jota tarvitaan kansainvälisen metsäteollisuusyrityksen loppukäyttäjävetoisessa liiketoiminnassa. Lisäksi tavoitteena on laatia kompetenssimalli, jota voidaan käyttää mm. rekrytoinnissa, koulutuksen ja työnkierron suunnittelussa. Tarkoituksena on tarkastella sekä tällä hetkellä että tulevaisuudessa tarvittavia ydinosaamisia. Työ keskittyy myyntihenkilöiden kompetenssien kuvaamiseen. Kirjallisuuden ja asiantuntijoiden haastattelujen avulla on selvitetty. kompetensseihin liittyviä asioita ja käsitteitä, kuten organisaation oppiminen, innovaatiot sekä asiakaslähtöisyys. Tämän jälkeen on kartoitettu case-yrityksen kartonkiyksikön myyntihenkilökunnan kompetensseja. Kompetenssikartoitus on tehty teemahaastattelujen avulla sekä lisäksi on käytetty työn aikana laadittua kompetenssimatriisia. Saatuja tuloksia on verrattu yhden asiakkaan näkemyksiin. Tulosten mukaan kolme tärkeintä tämän hetken kompetenssia ovat: holistinen näkemys asioista, suhteiden rakentaminen ja kielitaito. Tulevaisuuden tärkeimpiä kompetensseja puolestaan ovat: asiakaslähtöisyys, sähköinen kaupankäynti ja suhteiden rakentaminen. Lopuksi on käsitelty yleisiä metsäteollisuuden tulevaisuuden haasteita sekä annettu joitain kehitysideoita kompetenssien kehittämistä varten.

Ilmatorjuntaohjuksen laukaisualustan vaaitusjärjestelmän kehittäminen

Työn tavoitteena oli vaaitusjärjestelmän kehittäminen ITO 2005 Asrad-R –ohjusjärjestelmän laukaisualustalle. Järjestelmäkontin jokaiseen kulmaan suunniteltiin nostojalat, joita voitiin kääntää sekä nostaa ja laskea hydraulisesti. Järjestelmään kuului myös hydraulikäyttöinen asetaso, jonka ylä- ja ala-asennoilla oli erillinen lukitus. Tärkein vaadittu toiminto oli järjestelmäkontin vaaitus maan vetovoiman suhteen epätasaisella alustalla sekä maastossa että kuorma-auton päällä. Lisäksi tarvittiin nostojalkojen nostoliikkeelle toiminto, jolla konttia nostetaan ja lasketaan siten, että se säilyttää lähtökulmansa. Kaikkia nostojalkojen sylintereitä oli mahdollista käyttää myös yksittäin. Järjestelmällä oli kovat ympäristövaatimukset, koska se oli suunniteltu sotalaitteeksi rauhan ja kriisin aikaista toimintaa varten. Riittävät vapausasteet järjestelmän toimimiseksi ajoneuvon apurungon päällä saatiin nostojalkojen rotaatioliikkeen joustosta ja tassujen liukumisesta poikittain apurungon kiinnikkeissä. Maastossa nostojalat olivat täysin jäykkiä ja liukuminen tapahtui tassujen ja maalevyjen välillä. Hydraulijärjestelmässä käytettiin on/off-magneettiventtiilejä, koska liikkeet olivat hitaita ja vaadittuun tarkkuuteen ja nopeuteen päästiin helposti. Keskeisiä suunnittelun lähtökohtia olivat rakenteiden keveys, järjestelmän yksinkertaisuus, hinta ja toimintavarmuus. Yksinkertaisella ja edullisella järjestelmällä saatiin aikaan hyvin toimiva ratkaisu.

Multigenic lentiviral vectors for combined and tissue-specific expression of miRNA- and protein-based antiangiogenic factors.

Lentivirus-based gene delivery vectors carrying multiple gene cassettes are powerful tools in gene transfer studies and gene therapy, allowing coexpression of multiple therapeutic factors and, if desired, fluorescent reporters. Current strategies to express transgenes and microRNA (miRNA) clusters from a single vector have certain limitations that affect transgene expression levels and/or vector titers. In this study, we describe a novel vector design that facilitates combined expression of therapeutic RNA- and protein-based antiangiogenic factors as well as a fluorescent reporter from back-to-back RNApolII-driven expression cassettes. This configuration allows effective production of intron-embedded miRNAs that are released upon transduction of target cells. Exploiting such multigenic lentiviral vectors, we demonstrate robust miRNA-directed downregulation of vascular endothelial growth factor (VEGF) expression, leading to reduced angiogenesis, and parallel impairment of angiogenic pathways by codelivering the gene encoding pigment epithelium-derived factor (PEDF). Notably, subretinal injections of lentiviral vectors reveal efficient retinal pigment epithelium-specific gene expression driven by the VMD2 promoter, verifying that multigenic lentiviral vectors can be produced with high titers sufficient for in vivo applications. Altogether, our results suggest the potential applicability of combined miRNA- and protein-encoding lentiviral vectors in antiangiogenic gene therapy, including new combination therapies for amelioration of age-related macular degeneration.

Loanword Phonology, Lexical Exceptions, Morphologically Driven Underapplication, and the Nature of Positionally Biased Constraints

In this paper we provide a formal account for underapplication of vowel reduction to schwa in Majorcan Catalan loanwords and learned words. On the basis of the comparison of these data with those concerning productive derivation and verbal inflection, which show analogous patterns, in this paper we also explore the existing and not yet acknowledged correlation between those processes that exhibit a particular behaviour in the loanword phonology with respect to the native phonology of the language, those processes that show lexical exceptions and those processes that underapply due to morphological reasons. In light of the analysis of the very same data and taking into account the aforementioned correlation, we show how there might exist a natural diachronic relation between two kinds of Optimality Theory constraints which are commonly used but, in principle, mutually exclusive: positional faithfulness and contextual markedness constraints. Overall, phonological productivity is proven to be crucial in three respects: first, as a context of the grammar, given that «underapplication» is systematically found in what we call the productive phonology of the dialect (including loanwords, learned words, productive derivation and verbal inflection); second, as a trigger or blocker of processes, in that the productivity or the lack of productivity of a specific process or constraint in the language is what explains whether it is challenged or not in any of the depicted situations, and, third, as a guiding principle which can explain the transition from the historical to the synchronic phonology of a linguistic variety.

Internal material logistics development in customer-driven production

Työn tavoitteena oli synkronoida yleinen materiaalivirta tuotannon kanssa. Pyrkimyksenä oli virtaviivaistaa materiaalivirta, jotta materiaalin määrä, sekä turhat työvaiheet tuotantoalueella vähenisivät. Päämääränä oli vähentää materiaalilavojen määrää lattialla, sekä parantaa materiaalitoimitusten OTD (On-Time-Delivery) prosenttia.Teoreettinen osa käsittelee nykypäivän toimitusketjun tärkeimpiä elementtejä. Keskeisenä asiana perehdytään materiaalivirtaan ja sen tehokkaaseen hallintaan. Työ esittelee myös synkronisen johtamismallin periaatteet, sekä materiaalivirran synkronoimisen tuotannon kanssa.Empiirinen osuus kuvaa yrityksen materiaalihallinnan nykypäivän tilanteen, sen keskeiset ongelmat, sekä uuden toimintamalliehdotuksen. Työ esittelee kaksi pilottia, joiden tulokset varmistivat uuden virtaviivaistetun materiaalivirran ja täydennysmallin toimivuuden.Työn tulokset osoittavat, miten uusi materiaalin täydennysmalli vähentää materiaalilavojen, sekä jalostamattoman työn määrää tuotantoalueella.

Parallel feedback loops control the basal activity of the HOG MAPK signaling cascade.

Tight regulation of the MAP kinase Hog1 is crucial for survival under changing osmotic conditions. Interestingly, we found that Hog1 phosphorylates multiple upstream components, implying feedback regulation within the signaling cascade. Taking advantage of an unexpected link between glucose availability and Hog1 activity, we used quantitative single cell measurements and computational modeling to unravel feedback regulation operating in addition to the well-known adaptation feedback triggered by glycerol accumulation. Indeed, we found that Hog1 phosphorylates its activating kinase Ssk2 on several sites, and cells expressing a non-phosphorylatable Ssk2 mutant are partially defective for feedback regulation and proper control of basal Hog1 activity. Together, our data suggest that Hog1 activity is controlled by intertwined regulatory mechanisms operating with varying kinetics, which together tune the Hog1 response to balance basal Hog1 activity and its steady-state level after adaptation to high osmolarity.