Conservation of catchments: some theoretical considerations and case histories from Rio de Janeiro

Conservation has developed along two lines: protection of species and communities, and preservation of natural resources. Catchments provide the natural unit for conservation since they are the fundamental unit of terrestrial ecosystems and account for most of the flow of materials. Urban streams of the city of Rio de Janeiro are generally well protected in their headwaters by the large urban parks in steep terrain. However, the lower reaches are often very heavily impacted by sewage, channelling, etc. Fauna that require estuarine habitats for part of their life history are excluded from such streams. Ecosystem functioning in urban streams is probably changed through the loss of strongly-interacting shrimp. Leaf decomposition was found to be reduced in urban streams compared to pristine streams in one study. Conservation entities in the state of Rio de Janeiro tend to protect the mountainous areas; piedmont and coastal plain habitats are generally impacted by agriculture and habitation. Many attempts are being made to conserve catchments in the state of Rio de Janeiro; we discuss 4 case histories, which have different constraints and employ different strategies for management and conservation. Key words: connectivity, catadromous shrimp, conservation planning and management.Conservation has developed along two lines: protection of species and communities, and preservation of natural resources. Catchments provide the natural unit for conservation since they are the fundamental unit of terrestrial ecosystems and account for most of the flow of materials. Urban streams of the city of Rio de Janeiro are generally well protected in their headwaters by the large urban parks in steep terrain. However, the lower reaches are often very heavily impacted by sewage, channelling, etc. Fauna that require estuarine habitats for part of their life history are excluded from such streams. Ecosystem functioning in urban streams is probably changed through the loss of strongly-interacting shrimp. Leaf decomposition was found to be reduced in urban streams compared to pristine streams in one study. Conservation entities in the state of Rio de Janeiro tend to protect the mountainous areas; piedmont and coastal plain habitats are generally impacted by agriculture and habitation. Many attempts are being made to conserve catchments in the state of Rio de Janeiro; we discuss 4 case histories, which have different constraints and employ different strategies for management and conservation. Key words: connectivity, catadromous shrimp, conservation planning and management

O método dos elementos de contorno para a análise de fluco de calor unidimensional

Orientador : Prof. Dr. José Antônio Marques CarrerDissertação (mestrado) - Universidade Federal do Paraná, Setor de Ciências Exatas e Setor de Tecnologia, Programa de Pós-Graduação em Métodos Numéricos em Engenharia. Defesa: Curitiba, 18/03/2011Bibliografia: fls. 43-45Área de concentração: Mecanica computacionalResumo: Com o desenvolvimento da engenharia, tambem se desenvolveram metodos para resolucao de problemas relacionados a essa ciencia aplicada. Dada a dificuldade de obtencao de solucoes analiticas para as equacoes diferenciais que regem muitos problemas fisicos, surgiu a necessidade de se desenvolver metodos numericos para resolver esses problemas, ainda que de maneira aproximada. Com o desenvolvimento da informatica, as simulacoes numericas, entre elas o Metodo dos Elementos de Contorno (MEC), se tornaram uma poderosa ferramenta nas solucoes dos diversos problemas da engenharia. Para este trabalho, tendo em vista o exposto, foi desenvolvida uma formulacao do MEC para a solucao de problemas de propagacao de calor em dominios unidimensionais. Devido a utilizacao da solucao fundamental da estatica, uma integral de dominio, cujo integrando e igual ao produto da solucao fundamental com a derivada primeira do potencial em relacao ao tempo, aparece nas equacoes do MEC. Como a integral de dominio e mantida nas equacoes, essa formulacao e denominada MEC-D (onde a letra D esta representando o dominio). Alem da formulacao tradicional MEC-D, uma nova formulacao do MEC, baseada em uma ponderacao do tipo colocacao por subdominios, e proposta. Para validacao dos resultados, quatro exemplos sao apresentados e comparados com suas solucoes analiticas. Uma nova sera apresentada neste trabalho: considerando que as funcoes u e q possuem variacao linear no tempo, a equacao do MEC-D e integrada no intervalo de tempo [ tn , n 1 t ƒy ], gerando a formulacao designada MEC-T. Para as analises numericas foram desenvolvidos codigos computacionais em linguagem Fortran 2003.Abstract: Together with the development of engineering, also the methods for solving problems related to that applied science presented a remarkable development during the last decades. Due to the difficulty of obtaining analytical solutions to the differential equations that govern the physical problems, the numerical methods were developed in order to overtake such a difficulty. Among them, the Boundary Element Method has demonstrated to be very effective in solving many problems in the field of engineering. In this work, a BEM formulation was developed to the solution of heat conduction problems in one-dimensional problems. Due to the use of the static fundamental solution, a domain integral, whose integrand is equal to the product of fundamental solution with the first derivative of potential, appears in the BEM equations. Because this integral is kept in the equation, the result formulation is named D-BEM (D meaning domain). Beside the traditional D-BEM formulation, a new BEM formulation, based on sub-domain weighting residuals presented. For validation of results, four examples are presented and compared with the analytic solutions. Computer codes in Fortran 2003, were developed for the numerical analyses

Dynamic load balancing in parallel processing on non-homogeneous clusters

This paper analyzes the dynamic and static balancing of non-homogenous cluster architectures, simultaneously analyzing the theoretical parallel Speedup as well as the Speedup experimentally obtained. Three interconnected clusters have been used in which the machines within each cluster have homogeneous processors although different among clusters. Thus, the set can be seen as a 25-processor heterogeneous cluster or as a multi-cluster scheme with subsets of homogeneous processors. A classical application (Parallel N-Queens) with a parallel solution algorithm, where processing predominates upon communication, has been chosen so as to go deep in the load balancing aspects (dynamic or static) without distortion of results caused by communication overhead. At the same time, three forms of load distribution in the processors (Direct Static, Predictive Static and Dynamic by Demand) have been studied, analyzing in each case parallel Speedup and load unbalancing regarding problem size and the processors used.Facultad de Informátic

A Hybrid Parallel Neighbor-Joining Algorithm for Phylogenetic Tree Reconstruction on a Multicore Cluster

Building phylogenetic trees is one of the significant applications within bioinformatics, mainly due to its involvement in multiple sequence alignment. Because of the high computational complexity required, the use of parallel processing during the building process is convenient. Taking into account that current cluster architectures are hybrid, in this paper we present a parallel algorithm to build phylogenetic trees based on the Neighbor-Joining method, which uses a hybrid communication model (combination of message passing and shared memory), and then analyze its performance. Finally, conclusions and possible future lines of work are presentedFacultad de Informátic

Performance comparison of parallel programming paradigms on a multicore cluster

Currently, most supercomputers are multicore clusters. This type of architectures is said to be hybrid, because they combine distributed memory with shared memory. Traditional parallel programming paradigms (message passing and shared memory) cannot be naturally adapted to the hardware features offered by these architectures. A parallel paradigm that combines message passing with shared memory is expected to better exploit them. Therefore, in this paper the performance of two parallel programming paradigms (message passing and combination of message passing with shared memory) is analyzed for multicore clusters. The study case used is the construction of phylogenetic trees by means of the Neighbor-Joining method. Finally, conclusions and future research lines are presented.Facultad de Informátic

Performance comparison of parallel programming paradigms on a multicore cluster

Currently, most supercomputers are multicore clusters. This type of architectures is said to be hybrid, because they combine distributed memory with shared memory. Traditional parallel programming paradigms (message passing and shared memory) cannot be naturally adapted to the hardware features offered by these architectures. A parallel paradigm that combines message passing with shared memory is expected to better exploit them. Therefore, in this paper the performance of two parallel programming paradigms (message passing and combination of message passing with shared memory) is analyzed for multicore clusters. The study case used is the construction of phylogenetic trees by means of the Neighbor-Joining method. Finally, conclusions and future research lines are presented.Facultad de Informátic

A Hybrid Parallel Neighbor-Joining Algorithm for Phylogenetic Tree Reconstruction on a Multicore Cluster

Building phylogenetic trees is one of the significant applications within bioinformatics, mainly due to its involvement in multiple sequence alignment. Because of the high computational complexity required, the use of parallel processing during the building process is convenient. Taking into account that current cluster architectures are hybrid, in this paper we present a parallel algorithm to build phylogenetic trees based on the Neighbor-Joining method, which uses a hybrid communication model (combination of message passing and shared memory), and then analyze its performance. Finally, conclusions and possible future lines of work are presentedFacultad de Informátic

Teaching Concurrency and Parallelism Concepts with CMRE

Possible methodologies for teaching the concepts of processor heterogeneity and its impact on speedup and efficiency in a parallel system are discussed, as well as energy efficiency of parallel algorithms based on processor power. CMRE (Concurrent Multi Robot Environment) is expanded to be able to consider different virtual clocks in each robot (processor), as well as the cost – both in relation to time and energy consumption – of the operations carried out by the robots (Move, Put Down / Pick Up / Message / Inform). In this paper, we analyze some examples to show how concepts are introduced to students.Facultad de Informátic

Teaching Concurrency and Parallelism Concepts with CMRE

Possible methodologies for teaching the concepts of processor heterogeneity and its impact on speedup and efficiency in a parallel system are discussed, as well as energy efficiency of parallel algorithms based on processor power. CMRE (Concurrent Multi Robot Environment) is expanded to be able to consider different virtual clocks in each robot (processor), as well as the cost – both in relation to time and energy consumption – of the operations carried out by the robots (Move, Put Down / Pick Up / Message / Inform). In this paper, we analyze some examples to show how concepts are introduced to students.Facultad de Informátic

DNA sequence alignment: hybrid parallel programming on a multicore cluster

DNA sequence alignment is one of the most important operations of computational biology. In 1981, Smith and Waterman developed a method for sequences local alignment. Due to its computational power and memory requirements, various heuristics have been developed to reduce execution time at the expense of a loss of accuracy in the result. This is why heuristics do not ensure that the best alignment is found. For this reason, it is interesting to study how to apply the computer power of different parallel platforms to speed up the sequence alignment process without losing result accuracy. In this article, a new parallelization strategy (HI-M) of Smith-Waterman algorithm on a multi-core cluster is presented, configuring a pipeline with a hybrid communication model. Additionally, a performance analysis is carried out and compared with two previously presented parallel solutions. Finally, experimental results are presented, as well as future research lines.Facultad de Informátic