Porting and performance analysis of EC-Earth System on the BSC-MareNostrum Supercomputer

Earth System Models (ESM) have been successfuly developed over past few years, and are currently beeing used for simulating present day-climate, seasonal to interanual predictions of climate change. The supercomputer performance plays an important role in climate modeling since one of the challenging issues for climate modellers is to efficiently and accurately couple earth System components on present day computers architectures. At the Barcelona Supercomputing Center (BSC), we work with the EC- Earth System Model. The EC- Earth is an ESM, which currently consists of an atmosphere (IFS) and an ocean (NEMO) model that communicate with each other through the OASIS coupler. Additional modules (e.g. for chemistry and vegetation ) are under development. The EC-Earth ESM has been ported successfully over diferent high performance computin platforms (e.g, IBM P6 AIX, CRAY XT-5, Intelbased Linux Clusters, SGI Altix) at diferent sites in Europ (e.g., KNMI, ICHEC, ECMWF). The objective of the first phase of the project was to identify and document the issues related with the portability and performance of EC-Earth on the MareNostrum supercomputer, a System based on IBM PowerPC 970MP processors and run under a Linux Suse Distribution. EC-Earth was successfully ported to MareNostrum, and a compilation incompatibilty was solved by a two step compilation approach using XLF version 10.1 and 12.1 compilers. In addition, the EC-Earth performance was analyzed with respect to escalability and trace analysis with the Paravear software. This analysis showed that EC-Earth with a larger number of IFS CPUs (<128) is not feasible at the moment since some issues exists with the IFS-NEMO balance and MPI Communications.

A step-by-step tutorial to use HierFstat to analyse populations hierarchically structured at multiple levels.

The populations of parasites and infectious agents are most of the time structured in complex hierarchy that lies beyond the classical nested design described by Wright's F-statistics (F(IS), F(ST) and F(IT)). In this note we propose a user-friendly step-by-step notice for using recent software (HierFstat) that computes and test fixation indices for any hierarchical structure. We add some tricks and tips for some special data kind (haploid, single locus), some other procedure (bootstrap over loci) and how to handle crossed factors.

GeneID in "Drosophila"

GeneID is a program to predict genes in anonymous genomic sequences designed with a hierarchical structure. In the first step, splice sites, and start and stop codons are predicted and scored along the sequence using position weight matrices (PWMs). In the second step, exons are built from the sites. Exons are scored as the sum of the scores of the defining sites, plus the log-likelihood ratio of a Markov model for coding DNA. In the last step, from the set of predicted exons, the gene structure is assembled, maximizing the sum of the scores of the assembled exons. In this paper we describe the obtention of PWMs for sites, and the Markov model of coding DNA in Drosophila melanogaster. We also compare other models of coding DNA with the Markov model. Finally, we present and discuss the results obtained when GeneID is used to predict genes in the Adh region. These results show that the accuracy of GeneID predictions compares currently with that of other existing tools but that GeneID is likely to be more efficient in terms of speed and memory usage.

Archaeospicularia, new radiolarian order; a new step for the classification of the Lower Paleozoic Radiolaria.

A new radiolarian order - Archaeospicularia - is proposed for some Lower Paleozoic radiolarians previously considered to belong to Spumellaria and to Collodaria. It is characterized by a globular shell made of several spicules which can be free, interlocked, or fused to formed a latticed wall. The present paper gives the definition of this order and proposes a first classification. It is supposed that the Archaeospicularia represents the oldest radiolarian group and that in the Lower Paleozoic it gave rise to the orders Entactinaria, Albaillellaria, and probably Spumellaria by the reduction of the number of initial spicules. The origin of this order and its relationships with other groups of organisms with siliceous skeletons are also briefly discussed. (C) 2000 Academie des sciences / Editions scientifiques et medicales Elsevier SAS.

Towards the Fully Automatic Merging of Lexical Resources: A Step Forward

This article reports on the results of the research done towards the fully automatically merging of lexical resources. Our main goal is to show the generality of the proposed approach, which have been previously applied to merge Spanish Subcategorization Frames lexica. In this work we extend and apply the same technique to perform the merging of morphosyntactic lexica encoded in LMF. The experiments showed that the technique is general enough to obtain good results in these two different tasks which is an important step towards performing the merging of lexical resources fully automatically.

Occupational sex-composition and earnings : individual and social effects

This paper investigates the micro and macro-level factors affecting the empirical association between occupational sex-composition and individual earnings. This is done in two analytical steps using data from the second round of the European Social Survey. In a first step, country-fixed-effects regressions are used to test the extent to which job-specialization, gender attitudes and the relative supply of domestic work can account for the impact of occupational sex-composition on earnings. In accordance with previous research, it is found that all these micro-level variables have a significant effect on the analyzed association, yet only job-specialization can explain it away by itself. In a second analytical step, macro-level interactions are tested under the hypothesis that defamilialization policies reduce the pay-offs of sphere specialization by sex, generating incentives for all types of women to invest in the labor market. Empirical results suggest that gender attitudes and the relative supply of housework are much more loosely associated to earning in social-democratic and former communist societies than in conservative or liberal regimes. This finding is interpreted as consistent with the defamilialization hypothesis.

Temporary and circular labour migration : reassessing established public policies

Today, Temporary Labour Migration is a fundamental course of action promoted by relevant economic and political agents, such as EC, the GCIM, or the OECD. Based on a specific empirical case study of Temporary and Circular Labour Migration in the Catalonian agrarian sector, which has been distinguished as a particularly successful formula, we identify a new area of interest: the emergence of a new empirical migrant category, the Circular Labour Migrant, which remains theoretically unnamed and lacks public recognition. We argue that, until now, there have been two historical phases regarding temporary labour migration: one of total deregulation and another of partial regulation, led by private actors with support from public institutions, and featuring circularity. IN a developed Welfare State context, it would be normatively pertinent to except a step towards a third phase, one involving the institutionalization of this new mobility category through the elaboration of a public policy.

O fotojornalismo depois da fotografia: Modelos de configuração da cadeia produtiva do fotojornalismo em tempos de convergência digital

This research report concerns about the post-doctoral activities, conducted betweenSeptember 2010 and March 2011 at the University Pompeu Fabra, Barcelona. It comes to identify the consequences of the convergence phenomenon on photojournalism.Thus, in a more general approach, the effort is to to recovery the structural elements of the convergence concept in journalism. It aims to map, as well, the current debates about the repositioning of photographic practices linked to the news produced in a widespread adoption of digital devices in contemporary workflow. It is also specified,the analysis of photographic collectives as a result of the convergence frameworkapplied to photojournalism; the debate on ways of funding; alternatives facing thealleged crisis of press photography and, finally, proposes to create qualifying stages ofdevelopment of photojournalism in the digital age as well as the proposition of hypotheses concerning the structure of the productive routines. In addition, we present three cases to be analyzed in order to explore and verify the occurrence ofcharacteristics that may identify the object of research in the state of practice. Finally,we work in a series of conclusions, revisiting the main hypotheses. With this strategy, ispossible to define an sequence of analysis capable of addressing the characteristics present in the studied cases and other ones in future, thus, be able to affirm this stage as a step, in the continuous historical course of photojournalism.

Expression and one-step purification of Plasmodium proteins in dictyostelium.

Nearly full-length Circumsporozoite protein (CSP) from Plasmodium falciparum, the C-terminal fragments from both P. falciparm and P. yoelii CSP and a fragment comprising 351 amino acids of P.vivax MSPI were expressed in the slime mold Dictyostelium discoideum. Discoidin-tag expression vectors allowed both high yields of these proteins and their purification by a nearly single-step procedure. We exploited the galactose binding activity of Discoidin Ia to separate the fusion proteins by affinity chromatography on Sepharose-4B columns. Inclusion of a thrombin recognition site allowed cleavage of the Discoidin-tag from the fusion protein. Partial secretion of the protein was obtained via an ER independent pathway, whereas routing the recombinant proteins to the ER resulted in glycosylation and retention. Yields of proteins ranged from 0.08 to 3 mg l(-1) depending on the protein sequence and the purification conditions. The recognition of purified MSPI by sera from P. vivax malaria patients was used to confirm the native conformation of the protein expressed in Dictyostelium. The simple purification procedure described here, based on Sepharose-4B, should facilitate the expression and the large-scale purification of various Plasmodium polypeptides.

Quimera : com sonoritzar la bogeria

Aquest projecte consisteix en la producció sonora per a un curtmetratge. Des de la preproducció fins al disseny de so, s’analitzen i es realitzen tots els processos intermedis necessaris per arribar a tenir un producte audiovisual de qualitat i innovador. S’han desenvolupat diverses tasques: des del rodatge del curt, la composició de la banda sonora, fins a la mescla en 5.1, entre d’altres. En aquesta memòria es detalla pas a pas el procés que s’ha seguit per aconseguir el resultat que s’esperava, amb les reflexions prèvies i la investigació de les diverses opcions. L’objectiu principal és aprofundir en el camp del disseny sonor, i arribar a crear sons i efectes que impactin en l’espectador i no el deixin indiferent.

A new method for constructing exact tests without making any assumptions

We present a new method for constructing exact distribution-free tests (and confidence intervals) for variables that can generate more than two possible outcomes.This method separates the search for an exact test from the goal to create a non-randomized test. Randomization is used to extend any exact test relating to meansof variables with finitely many outcomes to variables with outcomes belonging to agiven bounded set. Tests in terms of variance and covariance are reduced to testsrelating to means. Randomness is then eliminated in a separate step.This method is used to create confidence intervals for the difference between twomeans (or variances) and tests of stochastic inequality and correlation.

Resolució de problemes i mètode de raonament en l'educació matemàtica

Des del principi dels temps històrics, la Matemàtica s'ha generat en totes les civilitzacions sobre la base de la resolució de problemes pràctics.Tanmateix, a partir del període grec la Història ens mostra la necessitat de fer un pas més endavant: l'evolució històrica de la Matemàtica situa els mètodes de raonament com a eix central de la recerca en Matemàtica. A partir d'una ullada als objectius i mètodes de treball d'alguns autors cabdals en la Història dels conceptes matemàtics postulem l'aprenentatge de les formes de raonament matemàtic com l'objectiu central de l'educació matemàtica, i la resolució de problemes com el mitjà més eficient per a coronar aquest objectiu.English version.From the beginning of the historical times, mathematics has been generated in all the civilizations on the base of the resolution of practical problems. Nevertheless, from the greek period History shows us the necessity to take one more step: the historical evolution of mathematics locates the methods of reasoning as the central axis of the research in mathematics. Glancing over the objectives and methods of work used bysome fundamental authors in the History of the mathematical concepts we postulated the learning of the forms of mathematical reasoning like the central objective of the mathematical education, and the resolution of problems as the most efficient way to carry out this objective.

Stepwise multiple testing as formalized data snooping

It is common in econometric applications that several hypothesis tests arecarried out at the same time. The problem then becomes how to decide whichhypotheses to reject, accounting for the multitude of tests. In this paper,we suggest a stepwise multiple testing procedure which asymptoticallycontrols the familywise error rate at a desired level. Compared to relatedsingle-step methods, our procedure is more powerful in the sense that itoften will reject more false hypotheses. In addition, we advocate the useof studentization when it is feasible. Unlike some stepwise methods, ourmethod implicitly captures the joint dependence structure of the teststatistics, which results in increased ability to detect alternativehypotheses. We prove our method asymptotically controls the familywise errorrate under minimal assumptions. We present our methodology in the context ofcomparing several strategies to a common benchmark and deciding whichstrategies actually beat the benchmark. However, our ideas can easily beextended and/or modied to other contexts, such as making inference for theindividual regression coecients in a multiple regression framework. Somesimulation studies show the improvements of our methods over previous proposals. We also provide an application to a set of real data.