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The Dune framework: Basic concepts and recent developments

Peter Bastian, Markus Blatt, Andreas Dedner, Nils-Arne Dreier, Christian Engwer, René Fritze, Carsten Gräser, Christoph Grüninger, Dominic Kempf, Robert Klöfkorn, Mario Ohlberger, Oliver Sander
2020 Computers and Mathematics with Applications  
. / Computers and Mathematics with Applications 81 (2021) Dune provides several implementations of grids all implementing the Dune-Grid interface.  ...  Dune-Grid: Abstract interface for general grids featuring any dimension, various element types, conforming and nonconforming, local hierarchical refinement, and parallel data decomposition.  ...  AlbertaGrid supports grid adaptation but cannot be used for parallel computations. A variety of applications make use of the Dune grid interface for adaptive computations.  ... 
doi:10.1016/j.camwa.2020.06.007 fatcat:37m6di54rbgo3m2y5y5m2hd234

The DUNE Framework: Basic Concepts and Recent Developments [article]

Peter Bastian, Markus Blatt, Andreas Dedner, Nils-Arne Dreier, Christian Engwer, René Fritze, Carsten Gräser, Christoph Grüninger, Dominic Kempf, Robert Klöfkorn, Mario Ohlberger, Oliver Sander
2020 arXiv   pre-print
of the first Dune version in 2007 and the main papers describing that state [1, 2].  ...  This discussion is accompanied with a description of various advanced features, such as coupling of domains and cut cells, grid modifications such as adaptation and moving domains, high order discretizations  ...  Acknowledgements We thank the Dune users and contributors for their continuous support, as only a vivid community unfolds the power of open source.  ... 
arXiv:1909.13672v3 fatcat:hc5a7al4xvhahdp7fs7f55cwg4

Lightweight, semi-automatic variability extraction: a case study on scientific computing

Alexander Grebhahn, Christian Kaltenecker, Christian Engwer, Norbert Siegmund, Sven Apel
2021 Empirical Software Engineering  
AbstractIn scientific computing, researchers often use feature-rich software frameworks to simulate physical, chemical, and biological processes.  ...  Commonly, researchers follow a clone-and-own approach: Copying the code of an existing, similar simulation and adapting it to the new simulation scenario.  ...  Acknowledgements This work has been supported by the German Research Foundation (DFG), as part of the Priority Programme 1648 "Software for Exascale Computing", under the contract AP 206/7 and Pervolution  ... 
doi:10.1007/s10664-020-09922-8 fatcat:yujaqyh2xbd27nlwsj7btuo5ke

High Energy Physics Forum for Computational Excellence: Working Group Reports (I. Applications Software II. Software Libraries and Tools III. Systems) [article]

Salman Habib, Robert Roser, Tom LeCompte, Zach Marshall, Anders Borgland, Brett Viren, Peter Nugent, Makoto Asai, Lothar Bauerdick, Hal Finkel, Steve Gottlieb, Stefan Hoeche (+13 others)
2015 arXiv   pre-print
As computational technology evolves rapidly in new directions, and data throughput and volume continue to follow a steep trend-line, it is important for the HEP community to develop an effective response  ...  In order to help shape the desired response, the HEP Forum for Computational Excellence (HEP-FCE) initiated a roadmap planning activity with two key overlapping drivers -- 1) software effectiveness, and  ...  Acknowledgments We record our thanks to our colleagues -too many to name individually -for extensive discussions and for assisting with this report in a number of places.  ... 
arXiv:1510.08545v1 fatcat:ligxzve2ifgphnsys5pbzy4vty

Exa-Dune – Flexible PDE Solvers, Numerical Methods and Applications [article]

Peter Bastian, Mirco Altenbernd, Nils-Arne Dreier, Christian Engwer, Jorrit Fahlke, René Fritze, Markus Geveler, Dominik Göddeke, Oleg Iliev, Olaf Ippisch, Jan Mohring, Steffen Müthing, Mario Ohlberger, Dirk Ribbrock, Nikolay Shegunov (+1 others)
2019 arXiv   pre-print
In the Exa-Dune project we have developed, implemented and optimised numerical algorithms and software for the scalable solution of partial differential equations (PDEs) on future exascale systems exhibiting  ...  a heterogeneous massively parallel architecture.  ...  We adopt this approach as a first principle in our MPI layer to handle asynchronous MPI operations and propose a highlevel C++ MPI interface, which we provide in D under the generic interface of Dune::  ... 
arXiv:1911.01492v2 fatcat:ureqbuj3pjfu3k27wayt7cu7xy

ComPASS : a tool for distributed parallel finite volume discretizations on general unstructured polyhedral meshes

E. Dalissier, C. Guichard, P. Havé, R. Masson, C. Yang, Stéphane Descombes, Bernard Dussoubs, Sylvain Faure, Loïc Gouarin, Violaine Louvet, Marc Massot, Vincent Miele
2013 ESAIM: Proceedings and Surveys  
The objective of the ComPASS project is to develop a parallel multiphase Darcy flow simulator adapted to general unstructured polyhedral meshes (in a general sense with possibly non planar faces) and to  ...  polyhedral mesh, the synchronization of the degrees of freedom, and the connection to scientific libraries including the partitioner METIS, the visualization tool PARAVIEW, and the parallel linear solver  ...  Acknowledgement The authors would like to thank the organisers of CEMRACS 2012 and especially Pierre Navaro for its precious help in using the package PETSc and running our code on the cluster of Marseille  ... 
doi:10.1051/proc/201343010 fatcat:nu4zv76z2zehxmf4zekstpckyq

Data Decomposition for Code Parallelization in Practice: What Do the Experts Need?

Anne Meade, Deva Kumar Deeptimahanti, Michael Johnston, Jim Buckley, J.J. Collins
2013 2013 IEEE 10th International Conference on High Performance Computing and Communications & 2013 IEEE International Conference on Embedded and Ubiquitous Computing  
Parallelizing serial software systems in order to run in a High Performance Computing (HPC) environment presents many challenges to developers.  ...  We discuss why existing tools have not been adopted in industry and based on our findings, provide a number of recommendations for future tool support.  ...  ACKNOWLEDGMENT We are grateful to the participants of the study for their time and enthusiasm.  ... 
doi:10.1109/hpcc.and.euc.2013.110 dblp:conf/hpcc/MeadeDJBC13 fatcat:uaghegnkkjb5nkxyfzseq3ukau

Deep Underground Neutrino Experiment (DUNE), Far Detector Technical Design Report, Volume II: DUNE Physics [article]

B. Abi, R. Acciarri, Mario A. Acero, G. Adamov, D. Adams, M. Adinolfi, Z. Ahmad, J. Ahmed, T. Alion, S. Alonso Monsalve, C. Alt, J. Anderson, C. Andreopoulos (+916 others)
2020 arXiv   pre-print
Volume II of this TDR, DUNE Physics, describes the array of identified scientific opportunities and key goals.  ...  This document also serves a wider purpose as a statement on the scientific potential of DUNE as a central component within a global program of frontier theoretical and experimental particle physics research  ...  A test spectrum input into the forward fitting algorithm produces a set of χ 2 values for every element in a grid.  ... 
arXiv:2002.03005v2 fatcat:k6pxhnzk6vfu3i5xijuzhcsmea

A Bottom-up approach to Grid-Computing at a University: the Black-Forest-Grid Initiative

R. Backofen, H.-G. Borrmann, W. Deck, A. Dedner, L. De Raedt, K. Desch, M. Diesmann, M. Geier, A. Greiner, W. R. Hess, J. Honerkamp, St. Jankowski (+13 others)
2006 PIK - Praxis der Informationsverarbeitung und Kommunikation  
1 Recent years have seen a rapid increase in the need for highperformance computing.  ...  We demonstrate that using state of the art grid computing technology the problem can now be addressed in a bottom-up approach.  ...  This observation suggests to define a common interface for the numerical schemes and to provide a generic implementation for central parts of the discretization.  ... 
doi:10.1515/piko.2006.81 fatcat:ntesur7nfndgtlyle4trttv4yi

A Scalable and Modular Software Architecture for Finite Elements on Hierarchical Hybrid Grids [article]

Nils Kohl, Dominik Thönnes, Daniel Drzisga, Dominik Bartuschat, and Ulrich Rüde
2018 arXiv   pre-print
In this article, a new generic higher-order finite-element framework for massively parallel simulations is presented.  ...  Combining an unstructured topology with structured grid refinement facilitates high geometric adaptability and matrix-free multigrid implementations with excellent performance.  ...  Acknowledgements This work was partly supported by the German Research Foundation through the Priority Programme 1648 "Software for Exascale Computing" (SPPEXA) and by grant WO671/11-1.  ... 
arXiv:1805.10167v1 fatcat:uxexq24lgjdgxp66mtvkyir5zy

Large scale simulation of pressure induced phase-field fracture propagation using Utopia

Patrick Zulian, Alena Kopaničáková, Maria Giuseppina Chiara Nestola, Andreas Fink, Nur Aiman Fadel, Joost VandeVondele, Rolf Krause
2021 CCF Transactions on High Performance Computing  
Complex numerical procedures can be expressed with few lines of code, and evaluated by different implementations, libraries, or computing hardware.  ...  Although in principle efficient iterative multi-level methods for these types of problems are available, they are not widely used in practice due to the complexity of their parallel implementation.  ...  The implementation documented in Heister et al. (2015) , and Klinsmann et al. (2015) relies on the package Deal II. Bangerth et al. (2007) and supports adaptive mesh refinement strategies.  ... 
doi:10.1007/s42514-021-00069-6 pmid:34993419 pmcid:PMC8679698 fatcat:h4dcvfuzgbb5thnydtqbefkcti

ParMooN—A modernized program package based on mapped finite elements

Ulrich Wilbrandt, Clemens Bartsch, Naveed Ahmed, Najib Alia, Felix Anker, Laura Blank, Alfonso Caiazzo, Sashikumaar Ganesan, Swetlana Giere, Gunar Matthies, Raviteja Meesala, Abdus Shamim (+2 others)
2017 Computers and Mathematics with Applications  
ParMooN is a program package for the numerical solution of elliptic and parabolic partial differential equations.  ...  Numerical studies, performed on compute servers, assess the efficiency of the parallelized geometric multigrid preconditioner in comparison with some parallel solvers that are available in the library  ...  A B C D A B C D (i) A B C D (ii) A B C D (iii) A B C D (iv) The implementation of the concepts described in this section have been adapted from MooNMD to ParMooN in a straightforward way.  ... 
doi:10.1016/j.camwa.2016.12.020 fatcat:quu6qexjtrfddiv2y3v7rqmpsa

ASCR/HEP Exascale Requirements Review Report [article]

Salman Habib, Robert Roser, Richard Gerber, Katie Antypas, Katherine Riley, Tim Williams, Jack Wells, Tjerk Straatsma, A. Almgren, J. Amundson, S. Bailey, D. Bard, K. Bloom (+39 others)
2016 arXiv   pre-print
be available at ASCR facilities, e) to build up and train a workforce capable of developing and using simulations and analysis to support HEP scientific research on next-generation systems.  ...  Appropriately configured leadership-class facilities can play a transformational role in enabling scientific discovery from these datasets. 4) A close integration of HPC simulation and data analysis will  ...  Tests of the MPI-parallel FFT have scaled up to ∼1 million MPI ranks for a 16,3843 grid.  ... 
arXiv:1603.09303v2 fatcat:5j4ovt4rmbg45jxjwyhdi5ozva

Celeritas: GPU-accelerated particle transport for detector simulation in High Energy Physics experiments [article]

S. C. Tognini, P. Canal, T. M. Evans, G. Lima, A. L. Lund, S. R. Johnson, S. Y. Jun, V. R. Pascuzzi, P. K. Romano
2022 arXiv   pre-print
This paper presents the planned roadmap for Celeritas, including its proposed code architecture, physics capabilities, and strategies for integrating it with existing and future experimental HEP computing  ...  In order to alleviate this impending computational bottleneck, the Celeritas MC particle transport code is designed to leverage the new generation of heterogeneous computer architectures, including the  ...  The ECP is a collaborative effort of two DOE organizations, the Office of Science and the National Nuclear Security Administration, that are responsible for the planning and preparation of a capable exascale  ... 
arXiv:2203.09467v2 fatcat:psq4sv2mhfaelann4je6pvtgza

Large scale simulation of pressure induced phase-field fracture propagation using Utopia [article]

Patrick Zulian and Alena Kopaničáková and Maria Giuseppina Chiara Nestola and Andreas Fink and Nur Aiman Fadel and Joost Vandevondele and Rolf Krause
2020 arXiv   pre-print
Complex numerical procedures can be expressed with few lines of code, and evaluated by different implementations, libraries, or computing hardware.  ...  Although in principle efficient iterative multi-level methods for these types of problems are available, they are not widely used in practice due to the complexity of their parallel implementation.  ...  The implementation documented in [57, 72] relies on the package Deal II. [11] and supports adaptive mesh refinement strategies.  ... 
arXiv:2007.12908v1 fatcat:x6wr4ekn6vaynpbzdzvzgscr2m
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