%0 Journal Article %1 Lange2015Flexible %A Lange, Michael %A Knepley, Matthew G. %A Gorman, Gerard J. %D 2015 %J arXiv Computer Science > Mathematical Software %K 55u05-abstract-complexes 65-01-numerical-analysis-instructional-exposition 65n50-pdes-bvps-mesh-generation-and-refinement 68n30-mathematical-aspects-of-software-engineering 68p05-data-structures 68p20-information-storage-and-retrieval exodusii firedrake gmsh petsc %N 1505.04633 %T Flexible, Scalable Mesh and Data Management using PETSc DMPlex %U http://arxiv.org/abs/1505.04633 %X Designing a scientific software stack to meet the needs of the next-generation of mesh-based simulation demands, not only scalable and efficient mesh and data management on a wide range of platforms, but also an abstraction layer that makes it useful for a wide range of application codes. Common utility tasks, such as file I/O, mesh distribution, and work partitioning, should be delegated to external libraries in order to promote code re-use, extensibility and software interoperability. In this paper we demonstrate the use of PETSc's DMPlex data management API to perform mesh input and domain partitioning in Fluidity, a large scale CFD application. We demonstrate that raising the level of abstraction adds new functionality to the application code, such as support for additional mesh file formats and mesh re- ordering, while improving simulation startup cost through more efficient mesh distribution. Moreover, the separation of concerns accomplished through this interface shifts critical performance and interoperability issues, such as scalable I/O and file format support, to a widely used and supported open source community library, improving the sustainability, performance, and functionality of Fluidity. %7 1

@article{Lange2015Flexible, abstract = {{Designing a scientific software stack to meet the needs of the next-generation of mesh-based simulation demands, not only scalable and efficient mesh and data management on a wide range of platforms, but also an abstraction layer that makes it useful for a wide range of application codes. Common utility tasks, such as file I/O, mesh distribution, and work partitioning, should be delegated to external libraries in order to promote code re-use, extensibility and software interoperability. In this paper we demonstrate the use of PETSc's DMPlex data management API to perform mesh input and domain partitioning in Fluidity, a large scale CFD application. We demonstrate that raising the level of abstraction adds new functionality to the application code, such as support for additional mesh file formats and mesh re- ordering, while improving simulation startup cost through more efficient mesh distribution. Moreover, the separation of concerns accomplished through this interface shifts critical performance and interoperability issues, such as scalable I/O and file format support, to a widely used and supported open source community library, improving the sustainability, performance, and functionality of Fluidity.}}, added-at = {2019-03-01T00:11:50.000+0100}, archiveprefix = {arXiv}, author = {Lange, Michael and Knepley, Matthew G. and Gorman, Gerard J.}, biburl = {https://www.bibsonomy.org/bibtex/2e37512e57262dc614cbcf1863d54b6fa/gdmcbain}, citeulike-article-id = {13987209}, citeulike-attachment-1 = {lange_15_flexible_1060383.pdf; /pdf/user/gdmcbain/article/13987209/1060383/lange_15_flexible_1060383.pdf; f09094908a7c34e56ab819cbc46291b37a70e4c6}, citeulike-linkout-0 = {http://arxiv.org/abs/1505.04633}, citeulike-linkout-1 = {http://arxiv.org/pdf/1505.04633}, day = 18, edition = 1, eprint = {1505.04633}, file = {lange_15_flexible_1060383.pdf}, interhash = {53556d5a66a24f6a0ab0300913ab4d18}, intrahash = {e37512e57262dc614cbcf1863d54b6fa}, journal = {arXiv Computer Science > Mathematical Software}, keywords = {55u05-abstract-complexes 65-01-numerical-analysis-instructional-exposition 65n50-pdes-bvps-mesh-generation-and-refinement 68n30-mathematical-aspects-of-software-engineering 68p05-data-structures 68p20-information-storage-and-retrieval exodusii firedrake gmsh petsc}, month = may, number = {1505.04633}, posted-at = {2016-03-24 11:35:06}, priority = {0}, timestamp = {2019-03-01T00:11:50.000+0100}, title = {Flexible, Scalable Mesh and Data Management using {PETSc} {DMPlex}}, url = {http://arxiv.org/abs/1505.04633}, year = 2015 }