Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 6

parallelization Related Publications

6 Using High Performance Computing for Online Flood Monitoring and Prediction

Authors: Stepan Kuchar, Michal Podhoranyi, Martin Golasowski, Radim Vavrik, Boris Sir, Jan Martinovic

Abstract:

The main goal of this article is to describe the online flood monitoring and prediction system Floreon+ primarily developed for the Moravian-Silesian region in the Czech Republic and the basic process it uses for running automatic rainfall-runoff and hydrodynamic simulations along with their calibration and uncertainty modeling. It takes a long time to execute such process sequentially, which is not acceptable in the online scenario, so the use of a high performance computing environment is proposed for all parts of the process to shorten their duration. Finally, a case study on the Ostravice River catchment is presented that shows actual durations and their gain from the parallel implementation.

Keywords: parallelization, flood prediction process, online flood prediction system, High performance computing

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5 Parallel Explicit Group Domain Decomposition Methods for the Telegraph Equation

Authors: Kew Lee Ming, Norhashidah Hj. Mohd. Ali

Abstract:

In a previous work, we presented the numerical solution of the two dimensional second order telegraph partial differential equation discretized by the centred and rotated five-point finite difference discretizations, namely the explicit group (EG) and explicit decoupled group (EDG) iterative methods, respectively. In this paper, we utilize a domain decomposition algorithm on these group schemes to divide the tasks involved in solving the same equation. The objective of this study is to describe the development of the parallel group iterative schemes under OpenMP programming environment as a way to reduce the computational costs of the solution processes using multicore technologies. A detailed performance analysis of the parallel implementations of points and group iterative schemes will be reported and discussed.

Keywords: parallelization, Telegraph equation, explicit group iterative scheme, domain decomposition algorithm

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4 Protein Secondary Structure Prediction Using Parallelized Rule Induction from Coverings

Authors: Leong Lee, Cyriac Kandoth, Jennifer L. Leopold, Ronald L. Frank

Abstract:

Protein 3D structure prediction has always been an important research area in bioinformatics. In particular, the prediction of secondary structure has been a well-studied research topic. Despite the recent breakthrough of combining multiple sequence alignment information and artificial intelligence algorithms to predict protein secondary structure, the Q3 accuracy of various computational prediction algorithms rarely has exceeded 75%. In a previous paper [1], this research team presented a rule-based method called RT-RICO (Relaxed Threshold Rule Induction from Coverings) to predict protein secondary structure. The average Q3 accuracy on the sample datasets using RT-RICO was 80.3%, an improvement over comparable computational methods. Although this demonstrated that RT-RICO might be a promising approach for predicting secondary structure, the algorithm-s computational complexity and program running time limited its use. Herein a parallelized implementation of a slightly modified RT-RICO approach is presented. This new version of the algorithm facilitated the testing of a much larger dataset of 396 protein domains [2]. Parallelized RTRICO achieved a Q3 score of 74.6%, which is higher than the consensus prediction accuracy of 72.9% that was achieved for the same test dataset by a combination of four secondary structure prediction methods [2].

Keywords: Data Mining, parallelization, protein secondary structure prediction

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3 Modeling and Simulations of Complex Low- Dimensional systems: Testing the Efficiency of Parallelization

Authors: Ryszard Matysiak, Grzegorz Kamieniarz

Abstract:

The deterministic quantum transfer-matrix (QTM) technique and its mathematical background are presented. This important tool in computational physics can be applied to a class of the real physical low-dimensional magnetic systems described by the Heisenberg hamiltonian which includes the macroscopic molecularbased spin chains, small size magnetic clusters embedded in some supramolecules and other interesting compounds. Using QTM, the spin degrees of freedom are accurately taken into account, yielding the thermodynamical functions at finite temperatures. In order to test the application for the susceptibility calculations to run in the parallel environment, the speed-up and efficiency of parallelization are analyzed on our platform SGI Origin 3800 with p = 128 processor units. Using Message Parallel Interface (MPI) system libraries we find the efficiency of the code of 94% for p = 128 that makes our application highly scalable.

Keywords: parallelization, Deterministic simulations, low-dimensional magnets, modeling of complex systems

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2 Strip Decomposition Parallelization of Fast Direct Poisson Solver on a 3D Cartesian Staggered Grid

Authors: Minh Vuong Pham, Frédéric Plourde, Son Doan Kim

Abstract:

A strip domain decomposition parallel algorithm for fast direct Poisson solver is presented on a 3D Cartesian staggered grid. The parallel algorithm follows the principles of sequential algorithm for fast direct Poisson solver. Both Dirichlet and Neumann boundary conditions are addressed. Several test cases are likewise addressed in order to shed light on accuracy and efficiency in the strip domain parallelization algorithm. Actually the current implementation shows a very high efficiency when dealing with a large grid mesh up to 3.6 * 109 under massive parallel approach, which explicitly demonstrates that the proposed algorithm is ready for massive parallel computing.

Keywords: parallelization, Strip-decomposition, fast directpoisson solver

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1 Problems of Boolean Reasoning Based Biclustering Parallelization

Authors: Marcin Michalak

Abstract:

Biclustering is the way of two-dimensional data analysis. For several years it became possible to express such issue in terms of Boolean reasoning, for processing continuous, discrete and binary data. The mathematical backgrounds of such approach — proved ability of induction of exact and inclusion–maximal biclusters fulfilling assumed criteria — are strong advantages of the method. Unfortunately, the core of the method has quite high computational complexity. In the paper the basics of Boolean reasoning approach for biclustering are presented. In such context the problems of computation parallelization are risen.

Keywords: parallelization, biclustering, Boolean reasoning, prime implicant

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