Configure Mixed Dimensional Branch with ParMETIS

installation
1

Hi all,

I am currently running @cdaversin’s mixed dimensional branch of FEniCS in Docker, and for (reasons) I need to use ParMETIS for mesh partitioning instead of SCOTCH.

I noticed, using the line

parameters["mesh_partitioner"] = "ParMETIS"

yields an error, saying DOLFIN has not been configured with support for ParMETIS.

Is there any way I can get ParMETIS support with the mixed dimensional branch on Docker?

Any help would be greatly appreciated,
Tim

2

You Need to build dolfin with parmetis support (for instance based on the dev images of dolfin), as we are not allowed to ship binaries of Parmetis; as explained by @jackhale on our slack:

The broader issue for the Docker images is that we cannot ship a binary of Parmetis (it is not Open Source by the definition of the Open Source Initiative). If someone wants Parmetis in a Docker image you will have to modify the Dockerfile and build the image yourself.

3

Hi dokken, thank you so much for your reply, and sorry for the delay in mine,

From some previous posts on the forum, am I right in saying that the master branch of DOLFIN now have the mixed dimensional features included? (I may be mistaken, as I do not have a huge amount of experience)

Therefore, can I simply build from the master branch with ParMETIS support and get the desired functionality?

Thanks,
Tim

4

That is correct.

Yes

5

From Bitbucket , there are a handful of fixes in Cecile’s mixed-dimensional branch that are not yet merged into master.

6

Hi dokken,

I tried to to build from source from
https://fenics.readthedocs.io/en/latest/installation.html
and also attempted using a docker script which you provided here (with no modifications at all)

Using a fresh install of Ubuntu 20.04 each time.
Both times, I got the error:

The following REQUIRED packages have not been found:
* UFC (required version >= 2019.2), Unified language for form-compilers (part of FFC), <https://bitbucket.org/fenics-project/ffc>

and error in big red lettering:

CMake Error at CMakeLists.txt:626 (message):
 Generation of form files failed:
 Traceback (most recent call last):...
 .
 .
 .
ImportError: cannot import name 'cellname2facetname' from 'ufl.cell'
(/usr/local/lib/python3.8/dist-packages/ufl/cell.py)

Unsure where I am going wrong, any advice would be super helpful,
Thanks

7

You should install the branch 2021.1.0 of ufl: GitHub - FEniCS/ufl at 2021.1.0
as the following commit Remove cellname2facetname by jpdean · Pull Request #77 · FEniCS/ufl · GitHub introduced non-backwards compatible changes.

8

Hi dokken,

Thanks for all you help! Built successfully and working now :slight_smile:

Regards,
Tim