A generic grid interface for parallel and adaptive scientific computing. Part II: implementation and tests in DUNE
In a companion paper (Bastian et al. 2007, this issue) we introduced an abstract definition of a parallel and adaptive hierarchical grid for scientific computing. Based on this definition we derive an efficient interface specification as a set of C++ classes. This interface separates the application...
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| Published in | Computing Vol. 82; no. 2-3; pp. 121 - 138 |
|---|---|
| Main Authors | , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
Vienna
Springer Vienna
01.07.2008
Springer Nature B.V |
| Subjects | |
| Online Access | Get full text |
| ISSN | 0010-485X 1436-5057 |
| DOI | 10.1007/s00607-008-0004-9 |
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| Abstract | In a companion paper (Bastian et al. 2007, this issue) we introduced an abstract definition of a parallel and adaptive hierarchical grid for scientific computing. Based on this definition we derive an efficient interface specification as a set of C++ classes. This interface separates the applications from the grid data structures. Thus, user implementations become independent of the underlying grid implementation. Modern C++ template techniques are used to provide an interface implementation without big performance losses. The implementation is realized as part of the software environment DUNE (
http://dune-project.org/
). Numerical tests demonstrate the flexibility and the efficiency of our approach. |
|---|---|
| AbstractList | In a companion paper (Bastian et al. 2007, this issue) we introduced an abstract definition of a parallel and adaptive hierarchical grid for scientific computing. Based on this definition we derive an efficient interface specification as a set of C++ classes. This interface separates the applications from the grid data structures. Thus, user implementations become independent of the underlying grid implementation. Modern C++ template techniques are used to provide an interface implementation without big performance losses. The implementation is realized as part of the software environment DUNE (http://dune-project.org/). Numerical tests demonstrate the flexibility and the efficiency of our approach. In a companion paper (Bastian et al. 2007, this issue) we introduced an abstract definition of a parallel and adaptive hierarchical grid for scientific computing. Based on this definition we derive an efficient interface specification as a set of C++ classes. This interface separates the applications from the grid data structures. Thus, user implementations become independent of the underlying grid implementation. Modern C++ template techniques are used to provide an interface implementation without big performance losses. The implementation is realized as part of the software environment DUNE ( http://dune-project.org/ ). Numerical tests demonstrate the flexibility and the efficiency of our approach. In a companion paper (Bastian et al. 2007, this issue) we introduced an abstract definition of a parallel and adaptive hierarchical grid for scientific computing. Based on this definition we derive an efficient interface specification as a set of C++ classes. This interface separates the applications from the grid data structures. Thus, user implementations become independent of the underlying grid implementation. Modern C++ template techniques are used to provide an interface implementation without big performance losses. The implementation is realized as part of the software environment DUNE (). Numerical tests demonstrate the flexibility and the efficiency of our approach. [PUBLICATION ABSTRACT] |
| Author | Dedner, A. Engwer, C. Ohlberger, M. Blatt, M. Sander, O. Klöfkorn, R. Bastian, P. Kornhuber, R. |
| Author_xml | – sequence: 1 givenname: P. surname: Bastian fullname: Bastian, P. organization: Institut für Parallele und Verteilte Systeme, Universität Stuttgart – sequence: 2 givenname: M. surname: Blatt fullname: Blatt, M. organization: Institut für Parallele und Verteilte Systeme, Universität Stuttgart – sequence: 3 givenname: A. surname: Dedner fullname: Dedner, A. organization: Abteilung für Angewandte Mathematik, Universität Freiburg – sequence: 4 givenname: C. surname: Engwer fullname: Engwer, C. organization: Institut für Parallele und Verteilte Systeme, Universität Stuttgart – sequence: 5 givenname: R. surname: Klöfkorn fullname: Klöfkorn, R. organization: Abteilung für Angewandte Mathematik, Universität Freiburg – sequence: 6 givenname: R. surname: Kornhuber fullname: Kornhuber, R. organization: Institut für Mathematik, Freie Universität Berlin – sequence: 7 givenname: M. surname: Ohlberger fullname: Ohlberger, M. organization: Institut für Numerische und Angewandte Mathematik, Universität Münster – sequence: 8 givenname: O. surname: Sander fullname: Sander, O. email: sander@mi.fu-berlin.de organization: Institut für Mathematik, Freie Universität Berlin |
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| Cites_doi | 10.1007/s00791-006-0013-1 10.1137/S1064827502405318 10.1016/0021-9991(84)90142-6 10.1016/B978-012387582-2/50040-X 10.1504/IJCSE.2008.021112 10.1002/nme.1620240206 10.1007/s007910050003 10.1007/s00607-008-0003-x 10.1007/s007910100051 10.1007/978-3-642-57172-5_2 10.1007/s00791-006-0053-6 10.1007/s00791-004-0140-5 |
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| References | SchmidtASiebertKDesign of adaptive finite element software—the finite element toolbox ALBERTA2005BerlinSpringer1068.65138 ZienkiewiczOZhuJA simple error estimator and adaptive procedure for practical engineering analysisInt J Numer Math Eng1987243373570602.7306310.1002/nme.1620240206875306 SickJLumsdaneALangtangenHBruasetAQuakEA modern framework for portable high-performance numerical linear algebraAdvances in software tools for scientific computing, vol 10. Lecture notes in computational science and engineering2000BerlinSpringer156 BastianPDroskeMEngwerCKlöfkornRNeubauerTOhlbergerMRumpfMKornhuberRHoppeRKeyesDPériauxJPironneauOXuJTowards a unified framework for scientific computingProceedings of the 15th conference on domain decomposition methods, no 40 in LNCSE2004BerlinSpringer167174 DUNE—distributed and unified numerics environment. http://dune-project.org Veldhuizen T (1999) Techniques for scientific C++. Technical report. http://extreme.indiana.edu/~tveldhui/papers/techniques Kornhuber R, Krause R, Sander O, Deuflhard P, Ertel S (2006) A monotone multigrid solver for two body contact problems in biomechanics. Comp Vis Sci (accepted for publication) Seymour J (1996) Views—a C++ standard template library extension. http://www.zeta.org.au/~jon/STL/views/doc/views.html Schupp B (1999) Entwicklung eines effizienten Verfahrens zur Simulation kompressibler Strömungen in 3D auf Parallelrechnern. PhD Thesis, Mathematische Fakultät, Universität Freiburg Young R, MacPhedran I Internet finite element resources. http://homepage.usask.ca/~ijm451/finite/fe_resources/fe_resources.html KrauseRSanderOAutomatic construction of boundary parametrizations for geometric multigrid solversComp Vis Sci20069112210.1007/s00791-006-0013-12214834 StallingDWesterhoffMHegeH-CHansenCJohnsonCAmira: a highly interactive system for visual data analysisThe visualization handbook, chap 382005AmsterdamElsevier74976710.1016/B978-012387582-2/50040-X Blatt M, Bastian P (2006) The iterative solver template library. In: Proceedings of the workshop on state-of-the-art in scientific and parallel computing. Lecture notes in scientific computing. Springer, Berlin (accepted) Bangerth W (2000) Using modern features of C++ for adaptive finite element methods: Dimension-independent programming in deal II. In: Deville M, Owens R (eds). Proceedings of the 16th IMACS world congress 2000, Lausanne, Switzerland, 2000. Document Sessions/118-1 Bastian P, Blatt M, Dedner A, Engwer C, Klöfkorn R, Ohlberger M, Sander O (2007) A generic grid interface for parallel and adaptive scientific computing. Part I. Abstract framework. Computing (this issue) (in preparation) Visible Human Project. http://www.nlm.nih.gov/research/visible/visible_human.html KrönerDNumerical schemes for conservation laws1997StuttgartWiley-Teubner0872.76001 VandevoordeDJosuttisNC++ templates—the complete guide2003USAAddison-Wesley WoodwardPColellaPThe numerical simulation of two-dimensional fluid flow with strong shocksJ Comput Phys1984541151730573.7605710.1016/0021-9991(84)90142-6748569 Blatt M, Bastian P (2007) On the generic parallelisation of iterative solvers for the finite element method. Int J Comput Sci Eng (submitted) Musser D, Derge G, Saini A (2001) STL tutorial and reference guide. Addison-Wesley, USA. ISBN 0-201-37923-6 Burri A, Dedner A, Klöfkorn R, Ohlberger M (2005) An efficient implementation of an adaptive and parallel grid in DUNE. Technical report, Submitted to: Proceedings of the 2nd Russian-German advanced research workshop on computational science and high performance computing, Stuttgart, March 14–16 ALUGrid Library. http://www.mathematik.uni-freiburg.de/IAM/Research/alugrid VeldhuizenTLangtangenHBruasetAQuakEBlitz++: the library that thinks it is a compilerAdvances in Software tools for scientific computing, vol 10. Lecture notes in computational science and engineering2000BerlinSpringer5787 GammaEHelmRJohnsonRVlissidesJDesign patterns: elements of reusable object-oriented software1995USAAddison-Wesley BastianPBirkenKJohannsenKLangSNeussNRentz-ReichertHWienersCUG—A flexible software toolbox for solving partial differential equationsComp Vis Sci1997127400970.6512910.1007/s007910050003 DednerARohdeCSchuppBWesenbergMA parallel, load balanced MHD code on locally adapted, unstructured grids in 3DComp Vis Sci2004779961120.763382088784 Eck C (1996) Existenz und Regularität der Lösungen für Kontaktprobleme mit Reibung. PhD Thesis, Universität Stuttgart WohlmuthBKrauseRMonotone methods on nonmatching grids for nonlinear contact problemsSIAM J Sci Comp20032513243470203022910.1137/S10648275024053182047208 PflaumCExpression templates for partial differential equationsComp Vis Sci200141180996.6511710.1007/s007910100051 B Wohlmuth (4_CR27) 2003; 25 C Pflaum (4_CR17) 2001; 4 D Vandevoorde (4_CR23) 2003 4_CR26 4_CR24 4_CR20 D Stalling (4_CR22) 2005 4_CR2 D Kröner (4_CR15) 1997 4_CR4 P Bastian (4_CR3) 1997; 1 4_CR6 4_CR19 4_CR7 4_CR8 A Schmidt (4_CR18) 2005 4_CR1 T Veldhuizen (4_CR25) 2000 A Dedner (4_CR9) 2004; 7 O Zienkiewicz (4_CR30) 1987; 24 4_CR16 4_CR13 4_CR11 4_CR10 E Gamma (4_CR12) 1995 P Woodward (4_CR28) 1984; 54 P Bastian (4_CR5) 2004 4_CR29 J Sick (4_CR21) 2000 R Krause (4_CR14) 2006; 9 |
| References_xml | – reference: Bangerth W (2000) Using modern features of C++ for adaptive finite element methods: Dimension-independent programming in deal II. In: Deville M, Owens R (eds). Proceedings of the 16th IMACS world congress 2000, Lausanne, Switzerland, 2000. Document Sessions/118-1 – reference: Schupp B (1999) Entwicklung eines effizienten Verfahrens zur Simulation kompressibler Strömungen in 3D auf Parallelrechnern. PhD Thesis, Mathematische Fakultät, Universität Freiburg – reference: Seymour J (1996) Views—a C++ standard template library extension. http://www.zeta.org.au/~jon/STL/views/doc/views.html – reference: Musser D, Derge G, Saini A (2001) STL tutorial and reference guide. Addison-Wesley, USA. ISBN 0-201-37923-6 – reference: ZienkiewiczOZhuJA simple error estimator and adaptive procedure for practical engineering analysisInt J Numer Math Eng1987243373570602.7306310.1002/nme.1620240206875306 – reference: SickJLumsdaneALangtangenHBruasetAQuakEA modern framework for portable high-performance numerical linear algebraAdvances in software tools for scientific computing, vol 10. Lecture notes in computational science and engineering2000BerlinSpringer156 – reference: Eck C (1996) Existenz und Regularität der Lösungen für Kontaktprobleme mit Reibung. PhD Thesis, Universität Stuttgart – reference: Veldhuizen T (1999) Techniques for scientific C++. Technical report. http://extreme.indiana.edu/~tveldhui/papers/techniques/ – reference: ALUGrid Library. http://www.mathematik.uni-freiburg.de/IAM/Research/alugrid/ – reference: Blatt M, Bastian P (2006) The iterative solver template library. In: Proceedings of the workshop on state-of-the-art in scientific and parallel computing. Lecture notes in scientific computing. Springer, Berlin (accepted) – reference: Kornhuber R, Krause R, Sander O, Deuflhard P, Ertel S (2006) A monotone multigrid solver for two body contact problems in biomechanics. Comp Vis Sci (accepted for publication) – reference: KrauseRSanderOAutomatic construction of boundary parametrizations for geometric multigrid solversComp Vis Sci20069112210.1007/s00791-006-0013-12214834 – reference: WohlmuthBKrauseRMonotone methods on nonmatching grids for nonlinear contact problemsSIAM J Sci Comp20032513243470203022910.1137/S10648275024053182047208 – reference: WoodwardPColellaPThe numerical simulation of two-dimensional fluid flow with strong shocksJ Comput Phys1984541151730573.7605710.1016/0021-9991(84)90142-6748569 – reference: PflaumCExpression templates for partial differential equationsComp Vis Sci200141180996.6511710.1007/s007910100051 – reference: BastianPBirkenKJohannsenKLangSNeussNRentz-ReichertHWienersCUG—A flexible software toolbox for solving partial differential equationsComp Vis Sci1997127400970.6512910.1007/s007910050003 – reference: Burri A, Dedner A, Klöfkorn R, Ohlberger M (2005) An efficient implementation of an adaptive and parallel grid in DUNE. Technical report, Submitted to: Proceedings of the 2nd Russian-German advanced research workshop on computational science and high performance computing, Stuttgart, March 14–16 – reference: DednerARohdeCSchuppBWesenbergMA parallel, load balanced MHD code on locally adapted, unstructured grids in 3DComp Vis Sci2004779961120.763382088784 – reference: GammaEHelmRJohnsonRVlissidesJDesign patterns: elements of reusable object-oriented software1995USAAddison-Wesley – reference: VandevoordeDJosuttisNC++ templates—the complete guide2003USAAddison-Wesley – reference: DUNE—distributed and unified numerics environment. http://dune-project.org/ – reference: Bastian P, Blatt M, Dedner A, Engwer C, Klöfkorn R, Ohlberger M, Sander O (2007) A generic grid interface for parallel and adaptive scientific computing. Part I. Abstract framework. Computing (this issue) (in preparation) – reference: SchmidtASiebertKDesign of adaptive finite element software—the finite element toolbox ALBERTA2005BerlinSpringer1068.65138 – reference: VeldhuizenTLangtangenHBruasetAQuakEBlitz++: the library that thinks it is a compilerAdvances in Software tools for scientific computing, vol 10. Lecture notes in computational science and engineering2000BerlinSpringer5787 – reference: Visible Human Project. http://www.nlm.nih.gov/research/visible/visible_human.html – reference: BastianPDroskeMEngwerCKlöfkornRNeubauerTOhlbergerMRumpfMKornhuberRHoppeRKeyesDPériauxJPironneauOXuJTowards a unified framework for scientific computingProceedings of the 15th conference on domain decomposition methods, no 40 in LNCSE2004BerlinSpringer167174 – reference: Blatt M, Bastian P (2007) On the generic parallelisation of iterative solvers for the finite element method. Int J Comput Sci Eng (submitted) – reference: Young R, MacPhedran I Internet finite element resources. http://homepage.usask.ca/~ijm451/finite/fe_resources/fe_resources.html – reference: StallingDWesterhoffMHegeH-CHansenCJohnsonCAmira: a highly interactive system for visual data analysisThe visualization handbook, chap 382005AmsterdamElsevier74976710.1016/B978-012387582-2/50040-X – reference: KrönerDNumerical schemes for conservation laws1997StuttgartWiley-Teubner0872.76001 – ident: 4_CR19 – start-page: 167 volume-title: Proceedings of the 15th conference on domain decomposition methods, no 40 in LNCSE year: 2004 ident: 4_CR5 – volume: 9 start-page: 11 year: 2006 ident: 4_CR14 publication-title: Comp Vis Sci doi: 10.1007/s00791-006-0013-1 – volume-title: Design of adaptive finite element software—the finite element toolbox ALBERTA year: 2005 ident: 4_CR18 – volume: 25 start-page: 324 issue: 1 year: 2003 ident: 4_CR27 publication-title: SIAM J Sci Comp doi: 10.1137/S1064827502405318 – volume: 54 start-page: 115 year: 1984 ident: 4_CR28 publication-title: J Comput Phys doi: 10.1016/0021-9991(84)90142-6 – volume-title: Numerical schemes for conservation laws year: 1997 ident: 4_CR15 – ident: 4_CR11 – ident: 4_CR29 – ident: 4_CR1 – start-page: 749 volume-title: The visualization handbook, chap 38 year: 2005 ident: 4_CR22 doi: 10.1016/B978-012387582-2/50040-X – ident: 4_CR7 doi: 10.1504/IJCSE.2008.021112 – volume-title: C++ templates—the complete guide year: 2003 ident: 4_CR23 – start-page: 1 volume-title: Advances in software tools for scientific computing, vol 10. Lecture notes in computational science and engineering year: 2000 ident: 4_CR21 – volume: 24 start-page: 337 year: 1987 ident: 4_CR30 publication-title: Int J Numer Math Eng doi: 10.1002/nme.1620240206 – volume: 1 start-page: 27 year: 1997 ident: 4_CR3 publication-title: Comp Vis Sci doi: 10.1007/s007910050003 – ident: 4_CR20 – ident: 4_CR16 – ident: 4_CR24 – ident: 4_CR4 doi: 10.1007/s00607-008-0003-x – ident: 4_CR10 – ident: 4_CR6 – ident: 4_CR2 – volume-title: Design patterns: elements of reusable object-oriented software year: 1995 ident: 4_CR12 – ident: 4_CR26 – volume: 4 start-page: 1 issue: 1 year: 2001 ident: 4_CR17 publication-title: Comp Vis Sci doi: 10.1007/s007910100051 – start-page: 57 volume-title: Advances in Software tools for scientific computing, vol 10. Lecture notes in computational science and engineering year: 2000 ident: 4_CR25 doi: 10.1007/978-3-642-57172-5_2 – ident: 4_CR8 – ident: 4_CR13 doi: 10.1007/s00791-006-0053-6 – volume: 7 start-page: 79 year: 2004 ident: 4_CR9 publication-title: Comp Vis Sci doi: 10.1007/s00791-004-0140-5 |
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