Mesh partition parameters (using MPI)

Question

Hi,
After some research on the forum i have found it is possible to control the way fenics partition the mesh (with MPI):

For exemple, to control the overlap between partitioned adjacent meshes, one can use:

parameters["ghost_mode"] = "shared_facet"

or

parameters["ghost_mode"] = "shared_vertex"  

Running some test case, i could see clearly the effect of each choice.

Then, i have noticed these two parameters:

parameters["mesh_partitioner"] = "SCOTCH"
parameters["partitioning_approach"] = "PARTITION"

So here is my question: what are "mesh_partitioner" and "partitioning_approach" doing ? And what are the different possible options for each of them? I don't know what are the other values i can set, apart SCOTCH and PARTITION, so i can't do any test.

Also, If you know any other parameter that control the mesh partitioning, please tell me.

I use Fenics 2016.1

Regards

Answer 1

You can specify ParMETIS instead if SCOTCH, if you have it installed. The 'approach' refers to ParMETIS mode, and has no effect on SCOTCH.

Comments

Thanks,

Thus, I have installed ParMETIS following the instructions there:

http://glaros.dtc.umn.edu/gkhome/metis/parmetis/download

And then i have re-run my program with the options:

parameters["mesh_partitioner"] = "ParMETIS"
parameters["partitioning_approach"] = "PARTITION"

And get this error:

    _mesh.UnitCubeMesh_swiginit(self, _mesh.new_UnitCubeMesh(*args))
RuntimeError: 

*** -------------------------------------------------------------------------
*** DOLFIN encountered an error. If you are not able to resolve this issue
*** using the information listed below, you can ask for help at
***
***     fenics-support@googlegroups.com
***
*** Remember to include the error message listed below and, if possible,
*** include a *minimal* running example to reproduce the error.
***
*** -------------------------------------------------------------------------
*** Error:   Unable to compute mesh partitioning using ParMETIS.
*** Reason:  DOLFIN has been configured without support for ParMETIS.
*** Where:   This error was encountered inside ParMETIS.cpp.
*** Process: 0
*** 
*** DOLFIN version: 2016.1.0
*** Git changeset:  unknown
*** -------------------------------------------------------------------------

Any clue?

---

You need to rebuild DOLFIN with ParMETIS.

---

Ok, Thanks,

I have only noticed we can let

parameters["ghost_mode"] = "none"

Visually, partitioned mesh created with 'none' and 'shared_vertex' are similar.
Then, what is the difference?

Although, in my code the option shared_vortex induced a segmentation error when i try to create the function space (on a imported submesh). By changing the option to 'none', the error disappeared.

Here is a separate post for this issue:
https://fenicsproject.org/qa/13109/import-submesh-code-create-associated-function-space-error?show=13155#a13155