restructuring pml demo

[Hawraa17]

I am working on restructuring pml demo to contribute to issue #3076

I would like to use this thread to address any issues as I work through the code.

Currently when I run the demo_pml.py demo, the code seems to freeze at the visualization producing only the output below with the figure attached. I am able to get the results line at the end of the demo if I remove the pyvista package. Any idea why the code is struggling to move forward, and if I should do anything to mitigate it?

I am using MacOS, conda environment with the complex build.

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Info    : Done meshing 1D (Wall 0.00579887s, CPU 0.009077s)
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Info    : Done meshing 2D (Wall 0.572483s, CPU 1.1574s)
Info    : 7765 nodes 16091 elements

[jorgensd]

I am working on restructuring pml demo to contribute to issue #3076

I would like to use this thread to address any issues as I work through the code.

Currently when I run the demo_pml.py demo, the code seems to freeze at the visualization producing only the output below with the figure attached. I am able to get the results line at the end of the demo if I remove the pyvista package. Any idea why the code is struggling to move forward, and if I should do anything to mitigate it?

I am using MacOS, conda environment with the complex build.

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Info    : [ 40%] Fragments - Performing Face-Face intersection                          
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Info    : [ 80%] Fragments - Making faces                                               
Info    : [ 90%] Fragments - Adding holes                                               
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Info    : [ 30%] Fragments - Performing Face-Face intersection                          
Info    : [ 70%] Fragments - Performing intersection of shapes                          
Info    : [ 80%] Fragments - Making faces                                               
Info    : [ 90%] Fragments - Adding holes                                               
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Info    : [ 80%] Fragments - Splitting faces                                            
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Info    : Done meshing 1D (Wall 0.00579887s, CPU 0.009077s)
Info    : Meshing 2D…
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Info    : Done meshing 2D (Wall 0.572483s, CPU 1.1574s)
Info    : 7765 nodes 16091 elements

What exact commands have you used to install DOLFINx through conda?
Additionally, are you running the demo from the main branch or the v0.10.0 release?

[Hawraa17]

I used
conda create -n env3-10-complex -c conda-forge python=3.10 fenics-dolfinx ‘petsc=*=complex*’ mpich
and I am running the demo from checkout version 0.10.0

[jorgensd]

conda create -n env3-10-complex -c conda-forge python=3.10 fenics-dolfinx ‘petsc=*=complex*’ mpich

Your conda environment does not include pyvista, scipy or gmsh. Is that on purpose?
When I additionally install scipy and python-gmsh using conda, the code runs for me.
Adding pyvista gives me me the following figure:

which I remove by pressing `q`, which lets the code run to the end and visualize the solution: which you can remove by again pressing `q`

[Hawraa17]

I just installed them after as well. Using q works, I get a similar figure. Thank you!

[Hawraa17]

@jorgensd
I wanted to share my current plan/sketch for the restructuring, let me know if you have any inputs:

The goal of restructuring is to improve readibility and reusability of the code for future implementation.
Convert the one liner codes starting after the post-processing into functions.

I would also like some advice on how I can run a test suite in the complex environment as I am running into the following error when running pytest python/test/

ERROR: /Users/Name/dolfinx/python/pyproject.toml: Cannot use both [tool.pytest] (native TOML types) and [tool.pytest.ini_options] (string-based INI format) simultaneously. Please use [tool.pytest] with native TOML types (recommended) or [tool.pytest.ini_options] for backwards compatibility.

Update : I removed ‘tool.pytest.ini_options’ from the pyproject.toml and was able to run the test, let me know if that is an ok move.

[jorgensd]

@jorgensd I wanted to share my current plan/sketch for the restructuring, let me know if you have any inputs:

The goal of restructuring is to improve readibility and reusability of the code for future implementation. Convert the one liner codes starting after the post-processing into functions.

I would also like some advice on how I can run a test suite in the complex environment as I am running into the following error when running pytest python/test/

ERROR: /Users/Name/dolfinx/python/pyproject.toml: Cannot use both [tool.pytest] (native TOML types) and [tool.pytest.ini_options] (string-based INI format) simultaneously. Please use [tool.pytest] with native TOML types (recommended) or [tool.pytest.ini_options] for backwards compatibility.

Update : I removed ‘tool.pytest.ini_options’ from the pyproject.toml and was able to run the test, let me know if that is an ok move.

You should update your branch, as it has been fixed in: #3978