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作者： Förster, Malte Kraus, Jiri Fraunhofer Institute for Algorithms and Scientific Computing SCAI Schloss Birlinghoven 53754 Sankt Augustin Germany

In many numerical simulation codes the backbone of the application covers the solution of linear systems of equations. Often, being created via a discretization of differential equations, the corresponding matrices are very sparse. One popular way to solve these sparse linear systems are multigrid methods-in particular AMG- because of their numerical scalability. But looking at modern multi-core architectures, also the parallel scalability has to be taken into account. With the memory bandwidth usually being the bottleneck of sparse matrix operations these linear solvers can't always benefit from increasing numbers of cores. To exploit the available aggregated memory bandwidth on larger scale NUMA machines evenly distributed data is often more an issue than load balancing. Additionally, using a threading model like OpenMP, one has to ensure the data locality manually by explicit placement of memory pages. On non uniform data it is always a tradeoff between these three principles, while the ideal strategy is strongly machine- and application dependent. In this paper we want to present some benchmarks of an AMG implementation based on a new performance library. Main focus is on the comparability to state-of-the-art solver packages regarding sequential performance as well as parallel scalability on common NUMA machines. To maximize throughput on standard model problems, several thread and memory configurations have been evaluated. We will show that even on large scale multi-core architectures easy parallel programming models, like OpenMP, can achieve a competitive performance compared to more complex programming models. © Springer-Verlag 2011.

关键词： Matrix algebra

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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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Using LAMA for efficient AMG on hybrid clusters

Using LAMA for efficient AMG on hybrid clusters

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作者： Kraus, Jiri Förster, Malte Brandes, Thomas Soddemann, Thomas Fraunhofer Institute for Algorithms and Scientific Computing SCAI Schloss Birlinghoven 53754 Sankt Augustin Germany

In this paper, we describe the implementation of an AMG solver for a hybrid cluster that exploits distributed and shared memory parallelization and uses the available GPU accelerators on each node. This solver has been written by using LAMA (Library for Accelerated Math Applications). This library does not only provide an easy-to-use framework for solvers that might run on different devices with different matrix formats, but also comes with features to optimize and hide communication and memory transfers between CPUs and GPUs. These features are explained and their impact on the efficiency of the AMG solver is shown in this paper. The benchmark results show that an efficient use of hybrid clusters is even possible for multi-level methods like AMG where fast solutions are needed on all levels for multiple problem sizes. © 2012 Springer-Verlag.

关键词： Program processors

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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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Carl Adam Petri 1

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1000年

作者： Einar Smith

ISBN: (数字)9783662480939

ISBN: (纸本)9783662480922;9783662516836

The book presents the life and works of one of Germany's most famous computer scientists, Carl Adam Petri. It is written in a vivid and entertaining manner, providing an in-depth discussion of the background behind Petri's best-known contribution to computer science, the Petri net. In this way the book can be read as a first introduction to nets, but it also covers the theoretical, physical and philosophical foundations behind nets, thus facilitating a comprehensive understanding of the wider range of Petri's works. The book is intended for readers with a previous knowledge in computer science, as well as for “interested non-professionals”, who want to get to know a remarkable personality of contemporary science.

关键词： History of computing Mathematics, general Philosophy, general Theory of Computation

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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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Preconditioning for efficiently applying algebraic multigrid in fully implicit reservoir simulations

Preconditioning for efficiently applying algebraic multigrid...

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SPE Reservoir Simulation Symposium 2013

作者： Gries, Sebastian Stüben, Klaus Brown, Geoffrey L. Chen, Dingjun Collins, David A. Fraunhofer Institute for Algorithms and Scientific Computing SCAI Germany Computer Modelling Group Ltd. Canada

ISBN: (纸本)9781627480246

Fully implicit petroleum reservoir simulations result in huge, often very ill-conditioned linear systems of equations to solve for different unknowns, for example, pressure and saturations. It is well known that the full system matrix contains both hyperbolic as well as nearly elliptic sub-systems. Since the solution of the coupled system is mainly determined by the solution of their elliptic (typically pressure) components, (CPR-type) two-stage preconditioning methods still belong to the most popular approaches to tackle such coupled systems. After a suitable extraction and decoupling, the numerically most costly step in such two-stage methods consists in solving these elliptic sub-systems. It is known that algebraic multigrid (AMG) provides a technique to solve elliptic linear equations very efficiently. The main advantage of AMG-based solvers - their numerical scalability - makes them particularly efficient for solving huge linear systems. Depending on the application, the system's properties range from simple to highly indefinite. Unfortunately decoupling pressure and saturation related parts may introduce further difficulties. Consequently, in complex industrial simulations, the application of AMG to elliptic sub-systems might not be straightforward. In fact, an important goal in defining an efficient two-stage preconditioning strategy consists in extracting elliptic sub-systems that are suitable for an efficient AMG solution and, at the same time, ensure a fast overall convergence of the two-stage approach. The importance of this will be demonstrated for several industrial cases. In particular, some of these cases are very hard to solve by AMG if applied in a standard way. Preliminary results for a CPR-type coupling of SAMG to CMG's PARASOL, a variable degree variable ordering ILU preconditioner using FGMRES, are compared to using PARASOL by itself. Alternative preconditioning operators will be presented giving elliptic sub-systems which are not only more suit

关键词： Iterative methods

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Predicting dementia in people with Parkinson’s disease

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npj Parkinson's Disease 2025年第1期11卷 1-10页

作者： Aborageh, Mohamed Hähnel, Tom Martins Conde, Patricia Klucken, Jochen Fröhlich, Holger Department of Bioinformatics Fraunhofer Institute for Algorithms and Scientific Computing (SCAI) Augustin Sankt 53757 Germany Department of Neurology University Hospital and Faculty of Medicine Carl Gustav Carus TUD Dresden University of Technology Dresden Germany Luxembourg Centre for Systems Biomedicine (LCSB) University of Luxembourg Esch-sur-Alzette Luxembourg Centre Hospitalier de Luxembourg (CHL) Luxembourg Luxembourg Bonn-Aachen International Center for Information Technology (B-IT) Rheinische Friedrich-Wilhelms-Universität Bonn Bonn 53115 Germany

Parkinson’s disease (PD) exhibits a variety of symptoms, with approximately 25% of patients experiencing mild cognitive impairment and 45% developing dementia within ten years of diagnosis. Predicting this progression and identifying its causes remains challenging. Our study utilizes machine learning and multimodal data from the UK Biobank to explore the predictability of Parkinson’s dementia (PDD) post-diagnosis, further validated by data from the Parkinson’s Progression Markers Initiative (PPMI) cohort. Using Shapley Additive Explanation (SHAP) and Bayesian Network structure learning, we analyzed interactions among genetic predisposition, comorbidities, lifestyle, and environmental factors. We concluded that genetic predisposition is the dominant factor, with significant influence from comorbidities. Additionally, we employed Mendelian randomization (MR) to establish potential causal links between hypertension, type 2 diabetes, and PDD, suggesting that managing blood pressure and glucose levels in Parkinson’s patients may serve as a preventive strategy. This study identifies risk factors for PDD and proposes avenues for prevention. © The Author(s) 2025.

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Quantifying the local reliability of a sequence alignment

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PROTEIN ENGINEERING 1996年第2期9卷 127-132页

作者： Mevissen, HT Vingron, M German National Research Center for Computer Science (GMD) Institute for Algorithms and Scientific Computing (SCAI) SchlossBirlinghoven D-53754 St Augustin Germany

We present a method for attributing a measure of reliability to a residue pair in an optimal alignment of two protein sequences. Validation based on a database of structurally correct alignments [Pascarella and Argos (1992) Protein Engng, 5, 121-137] shows that correctly aligned parts of a sequence alignment systematically receive high scores in this measure, The higher the sequence similarity between two sequences, the larger is the fraction found of the correct parts of the alignment, We used these observations to design a program that draws a reliability curve along an optimal alignment reflecting the chances for each residue pair to be aligned correctly.

关键词： alignment reliability protein sequence alignment

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Flux difference splitting for three-dimensional steady incompressible Navier-Stokes equations in curvilinear co-ordinates

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INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN FLUIDS 1996年第4期23卷 347-366页

作者： Oosterlee, CW Ritzdorf, H German National Research Center for Information Technology Institute for Algorithms and Scientific Computing (GMD SCAI) Schloss Birlinghoven D-53754 St. Augustin Germany

A collocated discretization of the 3D steady incompressible Navier-Stokes equations based on a flux-difference-splitting formulation is presented. The discretization employs primitive variables of Cartesian velocity components and pressure. The splitting used here is a polynomial splitting introduced by Dick and Linden of Roe type. Second-order accuracy is obtained with the defect correction approach in which the state vector is interpolated with van Leer's K-scheme. The underlying solution technique to solve the discretized equations is a parallel multiblock multigrid method. Several 2D and 3D test problems such as driven cavity and channel flows are solved.

关键词： three-dimensional incompressible Navier-Stokes collocated grid curvilinear co-ordinates flux difference splitting defect correction multigrid

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