Disconnected mesh elements in a single mesh part when creating parallel mesh

[zhangchonglin]

• While using the print_pumipic_partition tool to create partitioned mesh that can be used in PUMIPic, the tool created partitioned mesh; but for some mesh parts, the mesh elements are disconnected. See below figure, mesh part numbered 5 (owner rank 5) has disconnected elements:

./print_pumipic_partition [model name] [serial mesh name] [number of desired mesh partitions] [output mesh partition file name *.ptn]

• With Cameron's @cwsmith help, I also tried the zsplit tool, which generated exactly the same partitioned mesh as print_pumipic_partition tool: for some mesh parts, the mesh elements are disconnected. This may be understandable since both tools used the Zoltan graph partitioning approach.

• Then using the fixDisconnected tool, I am able to fix the disconnected element issue from the above generated partitioned mesh.

With above tests, the working workflow to create mesh partition files that can be used in PUMIPic will be:

1. use zsplit to create parallel mesh from model file and serial mesh file, for example:

mpirun -np 4 ./zsplit [model name] [serial mesh name] [prefix of output parallel mesh name *.smb] [number of desired mesh partitions]

2. use fixDisconnected to fix issue with disconnected mesh element from the zsplit created parallel mesh, for example:

mpirun -n 4 ./fixDisconnected [model name] [prefix of parallel mesh file name *.smb] [output mesh folder]

3. create mesh partition files (*.ptn files) that is needed in PUMIPic using the parallel mesh *.smb files.

However, since print_pumipic_partition tool only accepts serial mesh, it is not clear how can we use the parallel mesh to create these needed *.ptn files.

[cwsmith]

As discussed offline, the disconnected parts are not causing pumipic to fail, but there are performance concerns.