Flexible, Scalable Mesh and Data Management using PETSc DMPlex
(May 18, 2015)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.