Add ExtendableFEM.jl benchmark implementation

[jpthiele]

This adds the benchmark implementation of the linear elastic Plate with a Hole using the julia package ExtendableFEM.jl.
Technically it now works with singularity containers but still contains some errors and problems.
Therefore I have not yet 'registered' it as a tool in the workflow config.

[joergfunger]

thanks for the first try. Is there already some command that allows to test how to run the tool? in the optimal case a (new) action that just takes e.g. a single mesh, instantiates the environment and computes some output.

[joergfunger]

not sure, but can we somehow outsource the analytical solution? For python, there is currently a general class that defines that, and converts using scipy to evaluable functions. (Not sure if we find something, but it would somehow be nice if the evaluation of the error metrics, or the comparison with the analytical solution, is not done in each tool separately, but that the tool provides some output (stresses, displacements) and then the error_metrics class is handling that computation? If you do not have a specific idea, I would suggest creating an issue.

[jpthiele]

As for usage: you will need to install singularity (propably through general linux package manager)
and then the command is

snakemake --use-conda --use-singularity --cores all --config tools=extendablefem

[srosenbu]

As for usage: you will need to install singularity (propably through general linux package manager) and then the command is

snakemake --use-conda --use-singularity --cores all --config tools=extendablefem

You can install apptainer (the new name of the singularity project) into the same conda-environment as snakemake https://anaconda.org/channels/conda-forge/packages/apptainer/overview. I have not used it together with snakemake, but i was able to run the dolfinx docker container inside a conda-environment. This would be better imo than using the system package manager.

There is also a package called singularity on conda-forge, but it has not been updated since 2022. In Snakemake --use-singularity and --use-apptainer do the same thing according to the docs

Edit If Snakemake does not install apptainer by default, we should probably ad it into the general environment file https://github.com/BAMresearch/NFDI4IngModelValidationPlatform/blob/main/environment_benchmarks.yml