Error message: UFLException: Expecting a FunctionSpace or FiniteElement.

[andreerhardt]

Dear Cécile, dear Henrik,

I am very interested in using fenics-beat. I have already experience with cbc-beat, but an older version by Marie, later launched by you both on github, is running on my M1. Now, I would like to use fenics-beat, but unfortunately, I get an error message when running the monodomain examples. I think something went wrong during the installation. However, I can't find the error.

I am using an iMac M1 with Anaconda and have installed FEniCS and fenics-beat as follows:
################################
conda create -n fenicsenv python=3.11
conda activate fenicsenv
conda install -c conda-forge spyder
conda install -c conda-forge fenics
conda install -c conda-forge matplotlib

conda install conda-forge::pytest
conda install conda-forge::h5py
conda install conda-forge::fenics-ufl-legacy

python3 -m pip install fenics-beat
python3 -m pip install cardiac-geometries
python3 -m pip install gotranx

pip install ldrb
################################

The error message is the following:

Expecting a FunctionSpace or FiniteElement.
Traceback (most recent call last):

File /opt/anaconda3/envs/fenicsenv/lib/python3.11/site-packages/spyder_kernels/py3compat.py:356 in compat_exec
exec(code, globals, locals)

File ~/Documents/Computational Physiology Python/fenics-beat-main/demos/endocardial_stimulation.py:328
main()

File ~/Documents/Computational Physiology Python/fenics-beat-main/demos/endocardial_stimulation.py:227 in main
arr = beat.utils.expand_layer(

File /opt/anaconda3/envs/fenicsenv/lib/python3.11/site-packages/beat/utils.py:57 in expand_layer
u = ufl.TrialFunction(V)

File /opt/anaconda3/envs/fenicsenv/lib/python3.11/site-packages/ufl_legacy/argument.py:157 in TrialFunction
return Argument(function_space, 1, part)

File /opt/anaconda3/envs/fenicsenv/lib/python3.11/site-packages/ufl_legacy/argument.py:51 in init
error("Expecting a FunctionSpace or FiniteElement.")

File /opt/anaconda3/envs/fenicsenv/lib/python3.11/site-packages/ufl_legacy/log.py:158 in error
raise self._exception_type(self._format_raw(*message))

UFLException: Expecting a FunctionSpace or FiniteElement.

Do you have any idea what I did wrong? I have the impression it might be related with ufl_legacy or its installation. The cbc-beat version 2019.1.2 (28.02.2022) which is running does not use ufl_legacy and with python 3.9. For fenics-beat the conda environment has the FEniCS version 2019.1.0, ufl_legacy (2022.3.0) and python 3.11.

Best,

André

[finsberg]

Hi André
I am very happy to hear that you think this project is interesting. My hope is that it can be a good replacement for cbcbeat, and I also plan to develop a FEniCSx version it, which will have more or less the same design.

Regarding your issue, I think the problem might be that the version of FEniCS you are using does not use ufl-legacy, which was introduced not so long ago (https://fenicsproject.discourse.group/t/announcement-ufl-legacy-and-legacy-dolfin/11583) but which is currently only used for the development version of legacy FEniCS. I think you might resolve the issue if you just skip installing ufl-legacy.

On that note, I would also like to mention that we maintain docker images with the development version of FEniCS here: https://github.com/scientificcomputing/packages/pkgs/container/fenics
as well as one package with also contains gmsh here:
https://github.com/scientificcomputing/packages/pkgs/container/fenics-gmsh
These images are also built for ARM, so they should work on you M1 mac as well. This is the way I usually run FEniCS locally.

[andreerhardt]

Hi Henrik,

thank you very much for your reply and suggestions. I tried it without ufl_legacy, however fenics-beat requires ufl_legacy and gives me an error without installing it.

The first issue was that I usually use python 3.9 since it is included in Xcode. I got the message:

TypeError: unsupported operand type(s) for |: 'type' and 'NoneType'

Therefore, I created a new environment with python 3.11, python 3.10 is at least required, but python 3.12 yields an error with ldrb. Then, the error that ufl_legacy is not known/installed appeared. That was the reason why in installed everything in the qay I mentioned above.

But, I see I may have to go with docker images, which I use on my MacBook Pro M3 :-) I will try to get fenics-beat running there :-)

Thank you very much. I am looking forward seeing fenicsx-beat in the future. As far as I can see, fenics-beat is writing already quite close to FEniCSx :-)

Many thanks again :-)

Best,

André

[finsberg]

I have made and update now (see #24) so I belive it should work both with ufl and ufl-legacy. I also fixed the type annotations so it should also work on python version 3.8 and above.

[andreerhardt]

Great. Thank you very much! It works now with python 3.9 and ufl, but a new error appears, which seems to be within dolfin (2019.1.0):

File /opt/anaconda3/envs/fenicsproject/lib/python3.9/site-packages/dolfin/fem/form.py:51 in init
function_spaces = [func.function_space()._cpp_object for func in form.arguments()]

File /opt/anaconda3/envs/fenicsproject/lib/python3.9/site-packages/dolfin/fem/form.py:51 in
function_spaces = [func.function_space()._cpp_object for func in form.arguments()]

AttributeError: 'Argument' object has no attribute 'function_space'

Sorry to keep bothering you! I try to figure out what is going wrong here.

[finsberg]

Yes, I can reproduce the error here: https://github.com/finsberg/fenics-beat/actions/runs/8846006693/job/24291024007. Not really sure why it happens, but it seems to not be a problem if you use the docker image.

[andreerhardt]

Many thanks, then I will try the docker image :-)