MDASH: a multi-core-enabled program for structure solution from powder diffraction data

The simulated annealing approach to structure solution from powder diffraction data, as implemented in the DASH program, is easily amenable to parallelization at the individual run level. Modest increases in speed of execution can therefore be achieved by executing individual DASH runs on the individual cores of CPUs.

Parallel implementation and one year experiments with the Danish Eulerian Model

Large scale air pollution models are powerful tools, designed to meet the increasing demand in different environmental studies. The atmosphere is the most dynamic component of the environment, where the pollutants can be moved quickly on far distnce. Therefore the air pollution modeling must be done in a large computational domain. Moreover, all relevant physical, chemical and photochemical processes must be taken into account. In such complex models operator splitting is very often applied in order to achieve sufficient accuracy as well as efficiency of the numerical solution. The Danish Eulerian Model (DEM) is one of the most advanced such models. Its space domain (4800 × 4800 km) covers Europe, most of the Mediterian and neighboring parts of Asia and the Atlantic Ocean. Efficient parallelization is crucial for the performance and practical capabilities of this huge computational model. Different splitting schemes, based on the main processes mentioned above, have been implemented and tested with respect to accuracy and performance in the new version of DEM. Some numerical results of these experiments are presented in this paper.

PDM 2006: Proceedings of the International Workshop on Data Mining

Recently major processor manufacturers have announced a dramatic shift in their paradigm to increase computing power over the coming years. Instead of focusing on faster clock speeds and more powerful single core CPUs, the trend clearly goes towards multi core systems. This will also result in a paradigm shift for the development of algorithms for computationally expensive tasks, such as data mining applications. Obviously, work on parallel algorithms is not new per se but concentrated efforts in the many application domains are still missing. Multi-core systems, but also clusters of workstations and even large-scale distributed computing infrastructures provide new opportunities and pose new challenges for the design of parallel and distributed algorithms. Since data mining and machine learning systems rely on high performance computing systems, research on the corresponding algorithms must be on the forefront of parallel algorithm research in order to keep pushing data mining and machine learning applications to be more powerful and, especially for the former, interactive. To bring together researchers and practitioners working in this exciting field, a workshop on parallel data mining was organized as part of PKDD/ECML 2006 (Berlin, Germany). The six contributions selected for the program describe various aspects of data mining and machine learning approaches featuring low to high degrees of parallelism: The first contribution focuses the classic problem of distributed association rule mining and focuses on communication efficiency to improve the state of the art. After this a parallelization technique for speeding up decision tree construction by means of thread-level parallelism for shared memory systems is presented. The next paper discusses the design of a parallel approach for dis- tributed memory systems of the frequent subgraphs mining problem. This approach is based on a hierarchical communication topology to solve issues related to multi-domain computational envi- ronments. The forth paper describes the combined use and the customization of software packages to facilitate a top down parallelism in the tuning of Support Vector Machines (SVM) and the next contribution presents an interesting idea concerning parallel training of Conditional Random Fields (CRFs) and motivates their use in labeling sequential data. The last contribution finally focuses on very efficient feature selection. It describes a parallel algorithm for feature selection from random subsets. Selecting the papers included in this volume would not have been possible without the help of an international Program Committee that has provided detailed reviews for each paper. We would like to also thank Matthew Otey who helped with publicity for the workshop.

Scaling up classification rule induction through parallel processing

The fast increase in the size and number of databases demands data mining approaches that are scalable to large amounts of data. This has led to the exploration of parallel computing technologies in order to perform data mining tasks concurrently using several processors. Parallelization seems to be a natural and cost-effective way to scale up data mining technologies. One of the most important of these data mining technologies is the classification of newly recorded data. This paper surveys advances in parallelization in the field of classification rule induction.

CDASH: a cloud-enabled program for structure solution from powder diffraction data

The simulated annealing approach to crystal structure determination from powder diffraction data, as implemented in the DASH program, is readily amenable to parallelization at the individual run level. Very large scale increases in speed of execution can be achieved by distributing individual DASH runs over a network of computers. The CDASH program delivers this by using scalable on-demand computing clusters built on the Amazon Elastic Compute Cloud service. By way of example, a 360 vCPU cluster returned the crystal structure of racemic ornidazole (Z0 = 3, 30 degrees of freedom) ca 40 times faster than a typical modern quad-core desktop CPU. Whilst used here specifically for DASH, this approach is of general applicability to other packages that are amenable to coarse-grained parallelism strategies.

Reuse-based test planning for core-based systems-on-chip

Electronic applications are currently developed under the reuse-based paradigm. This design methodology presents several advantages for the reduction of the design complexity, but brings new challenges for the test of the final circuit. The access to embedded cores, the integration of several test methods, and the optimization of the several cost factors are just a few of the several problems that need to be tackled during test planning. Within this context, this thesis proposes two test planning approaches that aim at reducing the test costs of a core-based system by means of hardware reuse and integration of the test planning into the design flow. The first approach considers systems whose cores are connected directly or through a functional bus. The test planning method consists of a comprehensive model that includes the definition of a multi-mode access mechanism inside the chip and a search algorithm for the exploration of the design space. The access mechanism model considers the reuse of functional connections as well as partial test buses, cores transparency, and other bypass modes. The test schedule is defined in conjunction with the access mechanism so that good trade-offs among the costs of pins, area, and test time can be sought. Furthermore, system power constraints are also considered. This expansion of concerns makes it possible an efficient, yet fine-grained search, in the huge design space of a reuse-based environment. Experimental results clearly show the variety of trade-offs that can be explored using the proposed model, and its effectiveness on optimizing the system test plan. Networks-on-chip are likely to become the main communication platform of systemson- chip. Thus, the second approach presented in this work proposes the reuse of the on-chip network for the test of the cores embedded into the systems that use this communication platform. A power-aware test scheduling algorithm aiming at exploiting the network characteristics to minimize the system test time is presented. The reuse strategy is evaluated considering a number of system configurations, such as different positions of the cores in the network, power consumption constraints and number of interfaces with the tester. Experimental results show that the parallelization capability of the network can be exploited to reduce the system test time, whereas area and pin overhead are strongly minimized. In this manuscript, the main problems of the test of core-based systems are firstly identified and the current solutions are discussed. The problems being tackled by this thesis are then listed and the test planning approaches are detailed. Both test planning techniques are validated for the recently released ITC’02 SoC Test Benchmarks, and further compared to other test planning methods of the literature. This comparison confirms the efficiency of the proposed methods.

Escalabilidade Paralela de um Algoritmo de Migração Reversa no Tempo (RTM) Pré-empilhamento

The seismic method is of extreme importance in geophysics. Mainly associated with oil exploration, this line of research focuses most of all investment in this area. The acquisition, processing and interpretation of seismic data are the parts that instantiate a seismic study. Seismic processing in particular is focused on the imaging that represents the geological structures in subsurface. Seismic processing has evolved significantly in recent decades due to the demands of the oil industry, and also due to the technological advances of hardware that achieved higher storage and digital information processing capabilities, which enabled the development of more sophisticated processing algorithms such as the ones that use of parallel architectures. One of the most important steps in seismic processing is imaging. Migration of seismic data is one of the techniques used for imaging, with the goal of obtaining a seismic section image that represents the geological structures the most accurately and faithfully as possible. The result of migration is a 2D or 3D image which it is possible to identify faults and salt domes among other structures of interest, such as potential hydrocarbon reservoirs. However, a migration fulfilled with quality and accuracy may be a long time consuming process, due to the mathematical algorithm heuristics and the extensive amount of data inputs and outputs involved in this process, which may take days, weeks and even months of uninterrupted execution on the supercomputers, representing large computational and financial costs, that could derail the implementation of these methods. Aiming at performance improvement, this work conducted the core parallelization of a Reverse Time Migration (RTM) algorithm, using the parallel programming model Open Multi-Processing (OpenMP), due to the large computational effort required by this migration technique. Furthermore, analyzes such as speedup, efficiency were performed, and ultimately, the identification of the algorithmic scalability degree with respect to the technological advancement expected by future processors

Arquiteturas eficientes para sensoriamento espectral e classificação automática de modulações usando características cicloestacionárias

The increasing demand for high performance wireless communication systems has shown the inefficiency of the current model of fixed allocation of the radio spectrum. In this context, cognitive radio appears as a more efficient alternative, by providing opportunistic spectrum access, with the maximum bandwidth possible. To ensure these requirements, it is necessary that the transmitter identify opportunities for transmission and the receiver recognizes the parameters defined for the communication signal. The techniques that use cyclostationary analysis can be applied to problems in either spectrum sensing and modulation classification, even in low signal-to-noise ratio (SNR) environments. However, despite the robustness, one of the main disadvantages of cyclostationarity is the high computational cost for calculating its functions. This work proposes efficient architectures for obtaining cyclostationary features to be employed in either spectrum sensing and automatic modulation classification (AMC). In the context of spectrum sensing, a parallelized algorithm for extracting cyclostationary features of communication signals is presented. The performance of this features extractor parallelization is evaluated by speedup and parallel eficiency metrics. The architecture for spectrum sensing is analyzed for several configuration of false alarm probability, SNR levels and observation time for BPSK and QPSK modulations. In the context of AMC, the reduced alpha-profile is proposed as as a cyclostationary signature calculated for a reduced cyclic frequencies set. This signature is validated by a modulation classification architecture based on pattern matching. The architecture for AMC is investigated for correct classification rates of AM, BPSK, QPSK, MSK and FSK modulations, considering several scenarios of observation length and SNR levels. The numerical results of performance obtained in this work show the eficiency of the proposed architectures

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.

Uma metodologia para o controle de seguranca dinamica de sistemas de energia eletrica

This work presents an algorithm for the security control of electric power systems using control actions like generation reallocation, determined by sensitivity analysis (linearized model) and optimization by neural networks. The model is developed taking into account the dynamic network aspects. The preventive control methodology is developed by means of sensitivity analysis of the security margin related with the mechanical power of the system synchronous machines. The reallocation power in each machine is determined using neural networks. The neural network used in this work is of Hopfield type. These networks are dedicated electric circuits which simulate the constraint set and the objective function of an optimization problem. The advantage of using these networks is the higher speed in getting the solutions when compared to conventional optimization algorithms due to the great convergence rate of the process and the facility of the method parallelization. Then, the objectives are: formulate and investigate these networks implementations in determining. The generation reallocation in digital computers. Aiming to illustrate the proposed methodology an application considering a multi-machine system is presented.

Técnicas de paralelização em GPGPU aplicadas em algoritmo para remoção de ruído multiplicativo

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

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

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

Migração usando equação da onda unidirecional de abertura arbitrária

Neste trabalho avaliamos uma classe de operadores de continuação de campos de onda, baseados em equações unidirecionais e com aplicação direta à migração sísmica. O método de representação de equações de onda unidirecionais, desenvolvido neste trabalho, é válido para abertura angular arbitrária, baseia-se no conceito de rigidez de um semiespaço, na transformação Dirichlet-Neumann e em sua discretização por elementos finitos. O método de construção dos operadores de continuação requer a introdução de variáveis auxiliares cujo número cresce em função da maior abertura angular desejada para o operador. Efetuamos a implementação no domínio do espaço e da frequência o que permite sua imediata paralelização. Baseados em experimentos numéricos, que avaliam a relação de dispersão e a resposta ao impulso do operador, propomos prescrições que permitem especificar o número de variáveis auxiliares e o passo de continuação para o operador de migração. A aplicação do algoritmo nos dados do modelo de domo salino da SEG-EAGE demonstra a capacidade do algoritmo em migrar refletores com forte mergulho em meios com forte variação lateral de velocidade.

An Efficient Parallel Algorithm for Multiple Sequence Similarities Calculation Using a Low Complexity Method

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