Paralelização da ferramenta de alinhamento de sequências MUSCLE para um ambiente distribuído

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Plataforma de simulação computacional paralela com base nos conceitos de relógios lógicos e tempo virtual

Pós-graduação em Ciência da Computação - IBILCE

A graphical tool for the tomographic characterisation of microstructural features on metal matrix composites

Research on the micro-structural characterization of metal-matrix composites uses X-ray computed tomography to collect information about the interior features of the samples, in order to elucidate their exhibited properties. The tomographic raw data needs several steps of computational processing in order to eliminate noise and interference. Our experience with a program (Tritom) that handles these questions has shown that in some cases the processing steps take a very long time and that it is not easy for a Materials Science specialist to interact with Tritom in order to define the most adequate parameter values and the proper sequence of the available processing steps. For easing the use of Tritom, a system was built which addresses the aspects described before and that is based on the OpenDX visualization system. OpenDX visualization facilities constitute a great benefit to Tritom. The visual programming environment of OpenDX allows an easy definition of a sequence of processing steps thus fulfilling the requirement of an easy use by non-specialists on Computer Science. Also the possibility of incorporating external modules in a visual OpenDX program allows the researchers to tackle the aspect of reducing the long execution time of some processing steps. The longer processing steps of Tritom have been parallelized in two different types of hardware architectures (message-passing and shared-memory); the corresponding parallel programs can be easily incorporated in a sequence of processing steps defined in an OpenDX program. The benefits of our system are illustrated through an example where the tool is applied in the study of the sensitivity to crushing – and the implications thereof – of the reinforcements used in a functionally graded syntactic metallic foam.

Simulation of free surface flows in a distributed memory environment

A parallel technique, for a distributed memory machine, based on domain decomposition for solving the Navier-Stokes equations in cartesian and cylindrical coordinates in two dimensions with free surfaces is described. It is based on the code by Tome and McKee (J. Comp. Phys. 110 (1994) 171-186) and Tome (Ph.D. Thesis, University of Strathclyde, Glasgow, 1993) which in turn is based on the SMAC method by Amsden and Harlow (Report LA-4370, Los Alamos Scientific Laboratory, 1971), which solves the Navier-Stokes equations in three steps: the momentum and Poisson equations and particle movement, These equations are discretized by explicit and 5-point finite differences. The parallelization is performed by splitting the computation domain into vertical panels and assigning each of these panels to a processor. All the computation can then be performed using nearest neighbour communication. Test runs comparing the performance of the parallel with the serial code, and a discussion of the load balancing question are presented. PVM is used for communication between processes. (C) 1999 Elsevier B.V. B.V. All rights reserved.

The Owner Share scheduler for a distributed system

In large distributed systems, where shared resources are owned by distinct entities, there is a need to reflect resource ownership in resource allocation. An appropriate resource management system should guarantee that resource's owners have access to a share of resources proportional to the share they provide. In order to achieve that some policies can be used for revoking access to resources currently used by other users. In this paper, a scheduling policy based in the concept of distributed ownership is introduced called Owner Share Enforcement Policy (OSEP). OSEP goal is to guarantee that owner do not have their jobs postponed for longer periods of time. We evaluate the results achieved with the application of this policy using metrics that describe policy violation, loss of capacity, policy cost and user satisfaction in environments with and without job checkpointing. We also evaluate and compare the OSEP policy with the Fair-Share policy, and from these results it is possible to capture the trade-offs from different ways to achieve fairness based on the user satisfaction. © 2009 IEEE.