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Add HDF5 geometry file format

Dave Moxey requested to merge dmoxey/nektar:feature/hdf5-mesh-div into master

This MR adds support for a HDF5-based input format in the MeshGraphHDF5 class. Concurrently, it adds support for the use of parallel graph partitioners (presently Pt-Scotch) to permit the faster partitioning of the mesh at simulation startup. The new format is available when compiling with NEKTAR_USE_MPI, NEKTAR_USE_SCOTCH and NEKTAR_USE_HDF5 enabled.

This merge request also addresses a number of small bugs/optimisations to facilitate the larger mesh sizes that this format will enable:

  • MeshPartition classes now accept a map of mesh entities, vs. a full MeshGraph, so that we don't need to construct elements a priori before partitioning.
  • Various mutexes inside NekFactory, NekManager and MemoryManager have been removed by default and will only be compiled if the NEKTAR_ENABLE_THREAD_SAFETY advanced CMake option is enabled.
  • Gmsh 4.0 file format fixes to support reading of the appropriate physical entities.
  • Optimisation improvements for NekMesh tetrahedral elements.
  • Optimisation improvements for the InputStar NekMesh reader.
Edited by Dave Moxey

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