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partmesh

============== A tool for preparing the partitioned mesh for OpenGeoSys (OGS) 5 (https://github.com/ufz/ogs5) for parallel computing. METIS is used as the partitioning application. Once the source code is compiled, one gets two executable files, partmesh and mpmetis. OGS5 must be compiled with a Cmake option of -DOGS_CONFIG=MPI or -DOGS_CONFIG=PETSC for the latest version, or an option of -DOGS_FEM_MPI=ON or -DOGS_FEM_PETSC=ON for the old version.

Compile

  1. get the source code by command git clone https://github.com/ufz/mesh_partition.git
  2. change directory to mesh_partition
  3. get the submodule of METIS by commands git submodule init && git submodule update
  4. run cmake and compile the source code

Usage:

Assuming that a mesh save in file foo.msh is going to be partitioned, a partitioning can be conducted as follows for two different OGS 5 compilations for parallel FEM computing.

For OGS5 Compiled with Cmake option -DOGS_CONFIG=MPI or -DOGS_FEM_MPI=ON for old version

  1. Convert the OGS mesh data to METIS input data

    partmesh --ogs2metis foo

  2. Partition mesh data

    [full path]/partmesh --metis2ogs -np 5 -s -e foo

    where option -s means to call mpmetis via sysem call to partition the mesh, and option -e means element wise partitioning. Alternatively, mpmetis can be run beforehand to save memory usage for large mesh, and then run parmesh without -s option. For example,

    [full path]/mpmetis foo.mesh 5

    [full path]/partmesh --metis2ogs -np 5 -e foo

    Option -ogsmsh can be used here to output the partitioned mesh data into files for Gmsh for visualization.

    Note, in this step the command must be run with its full path.

For OGS5 Compiled with Cmake option -DOGS_CONFIG=PETSC or -DOGS_FEM_PETSC=ON for old version

  1. Convert the OGS mesh data to METIS input data

    For modelling with linear elements (processes excluding deformation), run command

    partmesh --ogs2metis foo

    For modelling with quadratic elements (processes including deformation, e.g. M, TM, HM, H2M), run command partmesh --ogs2metis -q foo

    Option -q indicates quadratic element.

  2. Partition mesh data

    [full path]/partmesh --metis2ogs -np 5 -s -n foo

    where option -s means to call mpmetis via sysem call to partition the mesh, , and option -n means node wise partitioning. Option '-q' has to be selected if it is already used in the first step in converting OGS mesh data to METIS input data.

    Alternatively, mpmetis can be run beforehand to save memory usage for large mesh, and then run parmesh without -s option. For example,

    [full path]/mpmetis foo.mesh 5

    [full path]/partmesh --metis2ogs -np 5 -n foo

    Option -odom can be used here to output the partitioned mesh data into VTK files for visualization.

    Note, in this step the command must be run with its full path.

    Always, the full options of the tool can be displayed by run command partmesh --help.