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Contribution to better handling of irregular problems in HPF2

4th International Conference on Parallel Processing, Euro-Par 1998

作者： Brandes, Thomas Brégier, Frédéric Counilh, Marie Christine Roman, Jean GMD/SCAI Institute for Algorithms and Scientific Computing German National Research Center for Computer Science Schloss Birlinghoven 53754 St. Augustin Germany LaBRI ENSERB Université Bordeaux i 33405 Talence Cedex France

ISBN: (纸本)3540649522

In this paper, we present our contribution for handling irregular applications with HPF2. We propose a programming style of irregular applications close to the regular case, so that both compile-time and run-time techniques can be more easily performed. We use the well-known tree data structure to represent irregular data structures with hierarchical access, such as sparse matrices. This algorithmic representation avoids the indirections coming from the standard irregular programming style. We use derived data types of Fortran 90 to define trees and some approved extensions of HPF2 for their mapping. We also propose a run-time support for irregular applications with loop-carried dependencies that cannot be determined at compile-time. Then, we present the TriDenT library, which supports distributed trees and provides runtime optimizations based on the inspector/executor paradigm. Finally, we validate our contribution with experimental results on IBM SP2 for a sparse Cholesky factorization algorithm.

关键词： Trees (mathematics)

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Random generation of embedded graphs and an extension to Dobrushin uniqueness (extended abstract) 98

Random generation of embedded graphs and an extension to Dob...

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Proceedings of the thirtieth annual ACM symposium on Theory of computing

作者： Marcus Peinado Thomas Lengauer Institute for Algorithms and Scientific Computing German National Research Center for Information Technology (GMD) 53754 Sankt Augustin Germany and Internationl Computer Science Institute Berkeley California Institute for Algorithms and Scientific Computing German National Research Center for Information Technology (GMD) 53754 Sankt Augustin Germany

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Hiding cliques for cryptographic security 98

Hiding cliques for cryptographic security

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Proceedings of the ninth annual ACM-SIAM symposium on Discrete algorithms

作者： Ari Juels Marcus Peinado University of California at Berkely Institute for Algorithms and Scientific Computing German National Research Center for Information Technology (GMD) 53754 Sankt Augustin Germany

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CASP2 experiences with docking flexible ligands using FLEXX†

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Proteins: Structure, Function, and Bioinformatics 1998年第S1期29卷

作者： Bernd Kramer Matthias Rarey Thomas Lengauer German National Research Center for Information Technology (GMD) Institute for Algorithms and Scientific Computing (SCAI) Schloß Birlinghoven Germany

We have applied our docking program FLEXX to all eight CASP2 targets involving protein complexes with small ligands. Of the seven targets that were kept in the CASP2 experiment, we could solve two. We found important parts of the solution in four other examples, and were unsuccessful on the remaining example. This paper discusses all predictions in detail. Each of our prediction runs took just a few minutes of computer time on a standard workstation and could thus be demonstrated in real time at the CASP meeting. We believe that this speed is the prime strength of our program FLEXX. In quality, our predictions are competitive with those produced by other predictors. The experiment showed that possible objectives of improvement of the FLEXX program are to incorporate relevant aspects of receptor flexibility, deal with water molecules in the receptor pocket, allow for a postoptimization to refine favorable complexes, and improve the scoring function. Proteins, Suppl. 1:221–225, 1997. © 1998 Wiley-Liss, Inc.

关键词： molecular docking flexible docking protein–ligand interaction molecular flexibility conformational analysis drug design

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ADAPTIVE PARALLEL MULTIGRID SOLUTION OF 2D INCOMPRESSIBLE NAVIER–STOKES EQUATIONS

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International Journal for Numerical Methods in Fluids 1998年第9期24卷

作者： Jian Wu Hubert Ritzdorf Kees Oosterlee Barbara Steckel Anton Schüller Institute of Algorithms and Scientific Computing GMD—German Research Centre for Information Technology Schloss Birlinghoven D-53754 Sankt Augustin Germany

In this paper an adaptive parallel multigrid method and an application example for the 2D incompressible Navier–Stokes equations are described. The strategy of the adaptivity in the sense of local grid refinement in the multigrid context is the multilevel adaptive technique (MLAT) suggested by Brandt. The parallelization of this method on scalable parallel systems is based on the portable communication library CLIC and the message-passing standards: PARMACS, PVM and MPI. The specific problem considered in this work is a two-dimensional hole pressure problem in which a Poiseuille channel flow is disturbed by a cavity on one side of the channel. Near geometric singularities a very fine grid is needed for obtaining an accurate solution of the pressure value. Two important issues of the efficiency of adaptive parallel multigrid algorithms, namely the data redistribution strategy and the refinement criterion, are discussed here. For approximate dynamic load balancing, new data in the adaptive steps are redistributed into distributed memories in different processors of the parallel system by block remapping. Among several refinement criteria tested in this work, the most suitable one for the specific problem is that based on finite-element residuals from the point of view of self-adaptivity and computational efficiency, since it is a kind of error indicator and can stop refinement algorithms in a natural way for a given tolerance. Comparisons between different global grids without and with local refinement have shown the advantages of the self-adaptive technique, as this can save computer memory and speed up the computing time several times without impairing the numerical accuracy. © 1997 By John Wiley & Sons, Ltd. Int. J. Numer. Methods Fluids 24, 875–892, 1997.

关键词： adaptive parallel multigrid method local refinement criteria incompressible Navier–Stokes equations hole pressure problem

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Adaptive parallel multigrid solution of 2D incompressible Navier-Stokes equations

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INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN FLUIDS 1997年第9期24卷 875-892页

作者： Wu, J Ritzdorf, H Oosterlee, K Steckel, B Schuller, A Institute of Algorithms and Scientific Computing GMD—German Research Centre for Information Technology Schloss Birlinghoven D-53754 Sankt Augustin Germany [*]Institute of Algorithms and Scientific Computing German Research Centre for Information Technology Schloss Birlinghoven D-53754 Sankt Augustin Germany

In this paper an adaptive parallel multigrid method and an application example for the 2D incompressible Navier-Stokes equations are described. The strategy of the adaptivity in the sense of local grid refinement in the multigrid context is the multilevel adaptive technique (MLAT) suggested by Brandt. The parallelization of this method on scalable parallel systems is based on the portable communication library CLIC and the message-passing standards: PARMACS, PVM and MPI. The specific problem considered in this work is a two-dimensional hole pressure problem in which a Poiseuille channel flow is disturbed by a cavity on one side of the channel. Near geometric singularities a very fine grid is needed for obtaining an accurate solution of the pressure value. Two important issues of the efficiency of adaptive parallel multigrid algorithms, namely the data redistribution strategy and the refinement criterion, are discussed here. For approximate dynamic load balancing, new data in the adaptive steps are redistributed into distributed memories in different processors of the parallel system by block remapping. Among several refinement criteria tested in this work, the most suitable one for the specific problem is that based on finite-element residuals from the point of view of self-adaptivity and computational efficiency, since it is a kind of error indicator and can stop refinement algorithms in a natural way for a given tolerance. Comparisons between different global grids without and with local refinement have shown the advantages of the self-adaptive technique, as this can save computer memory and speed up the computing time several times without impairing the numerical accuracy. (C) 1997 By John Wiley & Sons, Ltd.

关键词： adaptive parallel multigrid method local refinement criteria incompressible Navier-Stokes equations hole pressure problem

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Multiple automatic base selection: Protein-ligand docking based on incremental construction without manual intervention

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JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN 1997年第4期11卷 369-384页

作者： Rarey, M Kramer, B Lengauer, T German National Research Center for Information Technology (gmd) Institute for Algorithms and Scientific Computing (SCAI) Schloss Birlinghoven D-53754 Sankt Augustin Germany German National Research Center for Information Technology (gmd) Institute for Algorithms and Scientific Computing (SCAI) Schloss Birlinghoven D-53754 Sankt Augustin Germany German National Research Center for Information Technology (gmd) Institute for Algorithms and Scientific Computing (SCAI) Schloss Birlinghoven D-53754 Sankt Augustin Germany

A possible way of tackling the molecular docking problem arising in computer-aided drug design is the use of the incremental construction method. This method consists of three steps: the selection of a part of a molecule a so-called base fragment, the placement of the base fragment into the active site of a protein, and the subsequent reconstruction of the complete drug molecule. Assuming that a part of a drug molecule is known, which is specific enough to be a good base fragment,the method is proven to be successful for a large set of docking examples. In addition, it leads to the fastest algorithms for flexible docking published so far. In most real-world applications of docking, large sets of ligands have to be tested for affinity to a given protein. Thus, manual selection of a base fragment is not practical. On the other hand, the selection of a base fragment is critical in that only few selections lead to a low-energy structure. We overcome this limitation by selecting a representative set of base fragments instead of a single one. In this paper, we present a set of rules and algorithms to automate this selection. In addition, we extend the incremental construction method to deal with multiple fragmentations of the drug molecule. Our results show that with multiple automated base selection, the quality of the docking predictions is almost as good as with one manually preselected base fragment. In addition, the set of solutions is more diverse and alternative binding modes with low scores are found. Although the run time of the overall algorithm increases, the method remains fast enough to search through large ligand data sets.

关键词： molecular docking flexible docking protein-ligand interaction molecular flexibility conformational analysis drug design

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Time-efficient flexible superposition of medium-sized molecules

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JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN 1997年第4期11卷 357-368页

作者： Lemmen, C Lengauer, T German National Research Center for Information Technology (gmd) Institute for Algorithms and Scientific Computing (SCAI) Schloss Birlinghoven D-53754 Sankt Augustin Germany German National Research Center for Information Technology (gmd) Institute for Algorithms and Scientific Computing (SCAI) Schloss Birlinghoven D-53754 Sankt Augustin Germany

We present an efficient algorithm for the structural alignment of medium-sized organic molecules. The algorithm has been developed for applications in 3D QSAR and in receptor modeling. The method assumes one of the molecules, the reference ligand, to be presented in the conformation that it adopts inside the receptor pocket. The second molecule, the test ligand, is considered to be flexible, and is assumed to be given in an arbitrary low-energy conformation. Ligand flexibility is modeled by decomposing the test ligand into molecular fragments, such that ring systems are completely contained in a single fragment. Conformations of fragments and torsional angles of single bonds are taken from a small finite set, which depends on the fragment and bond, respectively. The algorithm superimposes a distinguished base fragment of the test ligand onto a suitable region of the reference ligand and then attaches the remaining fragments of the test ligand in a step-by-step fashion. During this process, a scoring function is optimized that encompasses bonding terms and terms accounting for steric overlap as well as for similarity of chemical properties of both ligands. The algorithm has been implemented in the FLEXS system. To validate the quality of the produced results, we have selected a number of examples for which the mutual superposition of two ligands is experimentally given by the comparison of the binding geometries known from the crystal structures of their corresponding protein-ligand complexes. On more than two-thirds of the test examples the algorithm produces rms deviations of the predicted versus the observed conformation of the test ligand below 1.5 Angstrom. The run time of the algorithm on a single problem instance is a few minutes on a common-day workstation. The overall goal of this research is to drastically reduce run times, while limiting the inaccuracies of the model and the computation to a tolerable level.

关键词： structural alignment molecular superposition molecular similarity molecular flexibility drug design

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A GMRES-based plane smoother in multigrid to solve 3D anisotropic fluid flow problems

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JOURNAL OF COMPUTATIONAL PHYSICS 1997年第1期130卷 41-53页

作者： Oosterlee, CW German National Research Center for Information Technology Institute for Algorithms Scientific Computing (SCAI) Schloss Birlinghoven 53754 Sankt Augustin Germany

For a discretization of the 3D steady incompressible Navier-Stokes equations a solution method is presented for solving flow problems on stretched grids. The discretization is a vertex-centered finite volume discretization with a flux splitting approach for the convective terms. Second-order accuracy is obtained with the well-known defect correction technique (B. Koren, J. Comput Phys. 87, 25, 1990). The solution method used is multigrid, for which a plane smoother is presented for obtaining good convergence in flow domains with severely stretched grids. A matrix is set up in a plane, which is solved iteratively with a preconditioned GMRES method. Here, a stop criterion for GMRES is tested, which reduces the number of inner iterations compared to an ''exact'' plane solver without affecting the multigrid convergence rates. The performance of the solution method is shown for a Poisson model problem and for 3D incompressible channel flow examples. (C) 1997 Academic Press

关键词： Finite volume method

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Parallel 'Go with the winners' algorithms in the LogP model

Parallel 'Go with the winners' algorithms in the LogP model

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International Symposium on Parallel Processing

作者： M. Peinado T. Lengauer German National Research Center for Information Technology GMD Institute for Algorithms and Scientific Computing Sankt Augustin Germany

The authors parallelize the 'Go with the winners' algorithm of Aldous and Vazirani (1994) and analyze the resulting parallel algorithm in the LogP-model. The main issues in the analysis are load imbalances and communication delays. The result of the analysis is a practical algorithm which, under reasonable assumptions, achieves linear speedup. Finally, they analyze the algorithm for a concrete application: generating models of amorphous chemical structures.

关键词： Algorithm design and analysis Concrete Delay Chemical analysis Monte Carlo methods Approximation algorithms Polynomials Simulated annealing Information technology scientific computing

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