Clustered Gauss–Huard algorithm for the solution of Ax=b

Al-Towaiq, Mohammad H.

doi:10.1016/j.amc.2006.06.114

Cited by 4 publications

(2 citation statements)

References 13 publications

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“…Though they usually enjoy a faster convergence rate when compared to the Jacobi method, the standard implementation of these methods restricts their utilization for parallel computing due to the sequential nature of a requirement of using the most recently updated values in current iteration as soon as they are available. A variety of parallelization techniques 50–54 have been developed to parallelize the GS/SOR methods. In the DelPhi program, special techniques, namely the “checkerboard” ordering (also known as the “black-red” ordering) and contiguous memory mapping 25 , have been implemented previously in order to achieve better performance than the standard implements of the GS/SOR methods.…”

Section: Parallelization Schemementioning

confidence: 99%

Continuous development of schemes for parallel computing of the electrostatics in biological systems: Implementation in DelPhi

Petukh

et al. 2013

J Comput Chem

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Due to the enormous importance of electrostatics in molecular biology, calculating the electrostatic potential and corresponding energies has become a standard computational approach for the study of biomolecules and nano-objects immersed in water and salt phase or other media. However, the electrostatics of large macromolecules and macromolecular complexes, including nano-objects, may not be obtainable via explicit methods and even the standard continuum electrostatics methods may not be applicable due to high computational time and memory requirements. Here, we report further development of the parallelization scheme reported in our previous work (J Comput Chem. 2012 Sep 15; 33(24):1960–6.) to include parallelization of the molecular surface and energy calculations components of the algorithm. The parallelization scheme utilizes different approaches such as space domain parallelization, algorithmic parallelization, multi-threading, and task scheduling, depending on the quantity being calculated. This allows for efficient use of the computing resources of the corresponding computer cluster. The parallelization scheme is implemented in the popular software DelPhi and results in speedup of several folds. As a demonstration of the efficiency and capability of this methodology, the electrostatic potential and electric field distributions are calculated for the bovine mitochondrial supercomplex illustrating their complex topology which cannot be obtained by modeling the supercomplex components alone.

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Section: Parallelization Schemementioning

confidence: 99%

Continuous development of schemes for parallel computing of the electrostatics in biological systems: Implementation in DelPhi

Petukh

et al. 2013

J Comput Chem

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“…The effective mapping of matrix elements to processors is the key factor to efficient implementation of the algorithm in parallel. In this paper, we employ the general distribution functions suggested by Al-Towaiq [19] because it embrace a wide range of matrix distribution functions, namely column/row blocked, column/row cyclic, column/row block cyclic, and column and row ( or 2D) block cyclic layouts [20][21][22]. The main issues of choosing a mapping are the load balancing and communication time.…”

Section: Mapping the Matrix Elements Onto The Processorsmentioning

confidence: 99%

Parallel Implementation of the Gauss-Seidel Algorithm on <i>k</i>-Ary <i>n</i>-Cube Machine

Al-Towaiq¹

2013

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3-D Multistrands Inductor Modeling: Influence of Complex Geometrical Arrangements

Scapolan¹,

Gagnoud²,

Terrail³

2014

IEEE Trans. Magn.

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International audienceWe study multistrands inductors in the context of high-frequency induction processes. They present the advantage of reducing Joule losses compared with solid inductors. We remind why that type of cable seems to be promising and what electromagnetic effects are already identified. We have to understand precisely what happens inside the inductor. Numerical simulation of the electromagnetic behavior of these objects is complicated due to the complexity of their 3-D geometry and to the size of the generated numerical system. We have developed a 3-D electromagnetic software based on an integral methods using classical Biot and Savart law. We applied this model for the simulation of multistrands cables with helical arrangement of strands. Execution time is reduced by the parallelization of the system building and the solver. We present some results obtained with 3-D simulations using integral methods for different configurations

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Clustered Gauss–Huard algorithm for the solution of Ax=b

Cited by 4 publications

References 13 publications

Continuous development of schemes for parallel computing of the electrostatics in biological systems: Implementation in DelPhi

Continuous development of schemes for parallel computing of the electrostatics in biological systems: Implementation in DelPhi

Parallel Implementation of the Gauss-Seidel Algorithm on <i>k</i>-Ary <i>n</i>-Cube Machine

3-D Multistrands Inductor Modeling: Influence of Complex Geometrical Arrangements

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Clustered Gauss–Huard algorithm for the solution of Ax=b

Cited by 4 publications

References 13 publications

Continuous development of schemes for parallel computing of the electrostatics in biological systems: Implementation in DelPhi

Continuous development of schemes for parallel computing of the electrostatics in biological systems: Implementation in DelPhi

Parallel Implementation of the Gauss-Seidel Algorithm on &lt;i&gt;k&lt;/i&gt;-Ary &lt;i&gt;n&lt;/i&gt;-Cube Machine

3-D Multistrands Inductor Modeling: Influence of Complex Geometrical Arrangements

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Parallel Implementation of the Gauss-Seidel Algorithm on <i>k</i>-Ary <i>n</i>-Cube Machine