AspectGrid: Aspect-Oriented Fault-Tolerance in Grid Platforms

Migrating traditional scientific applications to computational Grids requires programming tools that can help programmers update application behaviour to this kind of platforms. Computational Grids are particularly suited for long running scientific applications, but they are also more prone to faults than desktop machines. The AspectGrid framework aims to develop methodologies and tools that can help Grid-enable scientific applications, particularly focusing on techniques based on aspect-oriented programming. In this paper we present the aspect-oriented approach taken in the AspectGrid framework to address faults in computational Grids. In the proposed approach, scientific applications are enhanced with fault-tolerance capability by plugging additional modules. The proposed technique is portable across operating systems and minimises the changes required to base applications

Pulsed-field gel electrophoresis studies of Rhizobiaceae

The migration properties of circular, covalently closed (ccc) and linear DNAs were studied in pulsed-field gel electrophoresis as a model system for resolving large plasmids in the Rhizobiaceae. The effects of varying pulse time and agarose concentration on the electrophoretic mobility cccDNAs, ranging from 2 kilobase pairs (kb) to 16 kb, was investigated. We used both field inversion gel electrophoresis (FIGE) and electrophoresis in contour-clamped homogeneous electric fields (CHEF); both ccc and linear molecules had a minimum mobility as a function of pulse time in a CHEF apparatus. Linear and cccDNAs of the same size were affected differently by pulse time. The electrophoretic mobility of cccDNAs was pulse-time dependent in both electrophoretic systems;We used pulsed-field gel electrophoresis (PFG) and statistical analysis of Rhizobiaceae DNA sequences from GENBANK to identify rare-cutting restriction endonucleases. By using FIGE and CHEF, the genome sizes of Rhizobium meliloti and Bradyrhizobium japonicum were calculated. Comparisons were made between the genomes of free-living and bacteroid forms. The stability of genomic fingerprints produced by rare-cutting enzymes was studied on B. japonicum DNA plugs. It seems likely that large-scale DNA rearrangements do not occur during B. japonicum bacteroid development, after dedifferentiation, or by maintenance on rich media;FIGE and digestion with rare-cutting restriction enzymes were used to compare the genomes of B. japonicum field isolates from the 123 serocluster, as well as serotype strains USDA 123, USDA 127, and USDA 129. Genomic fingerprints (or field inversion gel electrophoretic types (FIGETs)), produced by four restriction enzymes, showed a high degree of diversity in the sizes of restriction fragments. Isolates could be classified according to FIGETs, and this classification was correlated with a serological classification. Hybridization with a nifHD gene probe to FIGE gels of B. japonicum DNA revealed that restriction fragment length polymorphisms (RFLPs) existed within members of serocluster 123 and provided further evidence of the relatedness between members of serogroups 123 and 127

AspectGrid: aspect-oriented fault-tolerance in grid platforms

Migrating traditional scientific applications to computational Grids requires programming tools that can help programmers update application behaviour to this kind of platforms. Computational Grids are particularly suited for long running scientific applications, but they are also more prone to faults than desktop machines. The AspectGrid framework aims to develop methodologies and tools that can help Grid-enable scientific applications, particularly focusing on techniques based on aspect-oriented programming. In this paper we present the aspect-oriented approach taken in the AspectGrid framework to address faults in computational Grids. In the proposed approach, scientific applications are enhanced with fault-tolerance capability by plugging additional modules. The proposed technique is portable across operating systems and minimises the changes required to base applications

An aspect-oriented approach to fault-tolerance in grid platforms

Migrating traditional scientific applications to computational Grids requires programming tools that can help programmers to update application behaviour to this kind of platforms. Computational Grids are particularly suited for long running scientific applications, but they are also more prone to faults than desktop machines. The AspectGrid framework aims to develop methodologies and tools that can help to Grid-enable scientific applications, particularly focusing on techniques based on aspect-oriented programming. In this paper we present the aspect-oriented approach taken in the AspectGrid framework to address faults in computational Grids. In the proposed approach, scientific applications are enhanced with fault-tolerance capability by plugging additional modules. The proposed technique is portable across operating systems and minimises the changes required to base applications

Checkpoint and run-time adaptation with pluggable parallelisation

Enabling applications for computational Grids requires new approaches to develop applications that can effectively cope with resource volatility. Applications must be resilient to resource faults, adapting the behaviour to available resources. This paper describes an approach to application-level adaptation that efficiently supports application-level checkpointing. The key of this work is the concept of pluggable parallelisation, which localises parallelisation issues into multiple modules that can be (un)plugged to match resource availability. This paper shows how pluggable parallelisation can be extended to effectively support checkpointing and run-time adaptation. We present the developed pluggable mechanism that helps the programmer to include checkpointing in the base (sequential). Based on these mechanisms and on previous work on pluggable parallelisation, our approach is able to automatically add support for checkpointing in parallel execution environments. Moreover, applications can adapt from a sequential execution to a multi-cluster configuration. Adaptation can be performed by checkpointing the application and restarting on a different mode or can be performed during run-time. Pluggable parallelisation intrinsically promotes the separation of software functionality from fault-tolerance and adaptation issues facilitating their analysis and evolution. The work presented in this paper reinforces this idea by showing the feasibility of the approach and performance benefits that can be achieved.(undefined

AOmpLib: an aspect library for large-scale multi-core parallel programming

This paper introduces an aspect-oriented library aimed to support efficient execution of Java applications on multi-core systems. The library is coded in AspectJ and provides a set of parallel programming abstractions that mimics the OpenMP standard. The library supports the migration of sequential Java codes to multi-core machines with minor changes to the base code, intrinsically supports the sequential semantics of OpenMP and provides improved integration with object-oriented mechanisms. The aspect- oriented nature of library enables the encapsulation of parallelism-related code into well-defined modules. The approach makes the parallelisation and the maintenance of large-scale Java applications more manageable. Furthermore, the library can be used with plain Java annotations and can be easily extended with application- specific mechanisms in order to tune application performance. The library has a competitive performance, in comparison with traditional parallel programming in Java, and enhances programmability, since it allows an independent development of parallelism-related code.This work is funded by ERDF - European Regional Development Fund through the COMPETE Programme (operational programme for competitiveness) and by National Funds through the FCT - Fundação para a Ciência e a Tecnologia (Portuguese Foundation for Science and Technology) within projects FCOMP-01-0124-FEDER- 011413 and FCOMP-01-0124-FEDER-010152

Implementing an openMP-like standard with AspectJ

This paper presents an aspect-oriented library, coded in AspectJ, that aims to mimic the OpenMP standard for multicore program- ming in Java. Building the library on top of AspectJ intrinsically supports the sequential semantics of OpenMP. The library enables the use of parallelism related constructors in object-oriented sys- tems due to better compatibility with inheritance, making it more suitable to introduce parallelism into object-oriented frameworks. However, it requires more program refactoring than OpenMP di- rectives.This work is funded by ERDF - European Regional Development Fund through the COMPETE Programme (operational programme for competitiveness) and by National Funds through the FCT Fundação para a Ciência e a Tecnologia (Portuguese Foundation for Science and Technology) within project FCOMP-01-0124FEDER-010152 and FCOMP-01-0124-FEDER-011413

VIS³COS. III. Environmental effects on the star formation histories of galaxies at z ∼ 0.8 seen in [O II], Hδ, and D_n4000

We present spectroscopic observations of 466 galaxies in and around a superstructure at z ∼ 0.84 targeted by the VIMOS Spectroscopic Survey of a Supercluster in the COSMOS field (VIS³COS). We use [OII]λ3727, Hδ, and D_n4000 to trace recent, medium-, and long-term star formation histories and investigate the effect of stellar mass and local environment on them. By studying trends in individual and composite galaxy spectra, we find that stellar mass and environment play a role in the observed galactic properties. Galaxies with low stellar mass (10  11) shows an increase in Hδ absorption strengths in intermediate-density environments (e.g. filaments). Galaxies with intermediate stellar mass (10.5 <  log₁₀ (M⋆/M⊙) < 11) have similar Hδ absorption profiles in all environments, but show an indication of enhanced [OII] emission in intermediate-density environments. This indicates that field galaxies with low stellar mass and filament galaxies with high stellar mass are more likely to have experienced a recent burst of star formation, while galaxies of the intermediate stellar-mass show an increase of star formation at filament-like densities. We also find that the median [OII] equivalent width (|EW_([OII])|) decreases from 27 ± 2 Å to 2.0^(+0.5)_(−0.4) Å and D_n4000 increases from 1.09 ± 0.01 to 1.56 ± 0.03 with increasing stellar mass (from ∼10^(9.25) to ∼10^(11.35) M⊙). For the dependence on the environment, we find that at fixed stellar mass, |EW_([OII])| is tentatively lower in environments with higher density. We find for D_n4000 that the increase with stellar mass is sharper in denser environments, which indicates that these environments may accelerate galaxy evolution. Moreover, we find higher D_n4000 values in denser environments at fixed stellar mass, suggesting that galaxies are on average older and/or more metal rich in these dense environments. This set of tracers depicts a scenario where the most massive galaxies have, on average, the lowest specific star formation rates and the oldest stellar populations (age ≳ 1 Gyr, showing a mass-downsizing effect). We also hypothesize that the observed increase in star formation (higher EW_([OII]|), higher specific star formation rate) at intermediate densities may lead to quenching because we find that the quenched fraction increases sharply from the filament to cluster-like regions at similar stellar masses

Defensoria em ação nas favelas: relato de uma ação compartilhada no Complexo do Alemão

A população moradora de favelas e periferias conta com um antigo histórico de violação de direitos individuais e falta de acesso à justiça. Paralelamente, a Defensoria Pública existe há mais de 100 anos e tem como sua missão o auxílio aos hipossuficientes. Porém, nem todos conseguem acessar esse dispositivo de justiça. Por qual motivo? Esse trabalho é um relatório que tem como objetivo analisar o projeto Defensoria em Ação nas Favelas, fazendo uma leitura dos motivos de sua existência, sua execução e desenvolvimento, e alguns resultados. Tendo como foco o Complexo do Alemão, o estudo presente mostra como pode ser produtiva a aliança entre poder público e Organização da Sociedade Civil, juntando suas individualidades e aptidões em busca de um bem comum