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Various updates to cope with changes in interpolation points behavior (jorgensd#89)
* Various updates to cope with changes in interpolation points behavior and hdf5 zlib issues * Rename nightly tests * update Keira K(nightly) * Delete various duplicate installations * Debugg * More debug * Simplify CI * Update docker images
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‎.github/workflows/build-publish.yml

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build:
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# The type of runner that the job will run on
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runs-on: ubuntu-latest
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container: dokken92/dolfinx_custom:15072022
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container: dokken92/dolfinx_custom:10082022
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env:
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HDF5_MPI: "ON"
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# Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
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- uses: actions/checkout@v2
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- name: Reinstall hdf5 with zlib enabled
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run: |
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export HDF5_SERIES=1.12
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export HDF5_PATCH=2
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wget -nc --quiet https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${HDF5_SERIES}/hdf5-${HDF5_SERIES}.${HDF5_PATCH}/src/hdf5-${HDF5_SERIES}.${HDF5_PATCH}.tar.gz
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tar xfz hdf5-${HDF5_SERIES}.${HDF5_PATCH}.tar.gz
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cmake -G Ninja -DCMAKE_INSTALL_PREFIX=/usr/local -DCMAKE_BUILD_TYPE=Release -DHDF5_ENABLE_PARALLEL=on -DHDF5_ENABLE_Z_LIB_SUPPORT=on -B build-dir -S hdf5-${HDF5_SERIES}.${HDF5_PATCH}
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cmake --build build-dir
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cmake --install build-dir
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- name: Test complex notebooks in parallel
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run: |
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export PKG_CONFIG_PATH=/usr/local/dolfinx-complex/lib/pkgconfig:$PKG_CONFIG_PATH

‎.github/workflows/main-test.yml renamed to ‎.github/workflows/nightly.yml

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# This is a basic workflow to help you get started with Actions
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name: Test against DOLFINx main
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name: Test against DOLFINx nightly build
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# Controls when the action will run.
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on:
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test-against-master:
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# The type of runner that the job will run on
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runs-on: ubuntu-latest
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container: dolfinx/lab
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container: dolfinx/lab:nightly
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HDF5_MPI: "ON"
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- name: Install dependencies
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run: |
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pip3 install --upgrade pip setuptools
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CC=mpicc HDF_MPI="ON" HDF5_DIR="/usr/lib/x86_64-linux-gnu/hdf5/mpich/" pip3 install --no-cache-dir -r docker/requirements.txt
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CC=mpicc HDF_MPI="ON" HDF5_DIR="/usr/local/" pip3 install --no-cache-dir -r docker/requirements.txt
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apt-get -qq update
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apt-get install -y libgl1-mesa-dev xvfb nodejs
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apt-get clean
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rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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jupyter nbextension enable --py --sys-prefix ipygany
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rm -rf /usr/local/share/.cache/*
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jupyter-book -h
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- name: Test complex notebooks in parallel
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run: |
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export PKG_CONFIG_PATH=/usr/local/dolfinx-complex/lib/pkgconfig:$PKG_CONFIG_PATH

‎.vscode/c_cpp_properties.json

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"defines": [],
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"compilerPath": "/usr/bin/gcc",
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"cStandard": "c11",
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"cppStandard": "c++17",
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"cppStandard": "c++20",
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"intelliSenseMode": "clang-x64",
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"configurationProvider": "vector-of-bool.cmake-tools"
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}

‎Dockerfile

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FROM dokken92/dolfinx_custom:15072022
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FROM dokken92/dolfinx_custom:10082022
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# create user with a home directory
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ARG NB_USER

‎chapter1/complex_mode.ipynb

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{
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"data": {
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"application/vnd.jupyter.widget-view+json": {
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"model_id": "d78185ab2481475d8596d2e5cfa2f975",
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"model_id": "66c7da35aae94a36ba1d467abc3c2813",
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"version_major": 2,
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"version_minor": 0
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},
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{
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"data": {
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"application/vnd.jupyter.widget-view+json": {
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"model_id": "8594601f751740259e13087567cb8d79",
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"model_id": "5a0ab66cd1534a01b7c9accbb5195d17",
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"version_major": 2,
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‎chapter1/complex_mode.py

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# extension: .py
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# format_name: light
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# format_version: '1.5'
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# jupytext_version: 1.13.8
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# jupytext_version: 1.14.1
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# kernelspec:
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# display_name: Python 3 (DOLFINx complex)
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# language: python

‎chapter1/fundamentals_code.ipynb

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"\u001b[0m\u001b[2m2022-07-15 17:29:58.326 ( 0.450s) [ A689B000] vtkExtractEdges.cxx:435 INFO| \u001b[0mExecuting edge extractor: points are renumbered\u001b[0m\n",
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"\u001b[0m\u001b[2m2022-07-15 17:29:58.327 ( 0.451s) [ A689B000] vtkExtractEdges.cxx:551 INFO| \u001b[0mCreated 144 edges\u001b[0m\n"
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"\u001b[0m\u001b[2m2022-08-02 20:46:58.678 ( 0.504s) [ E9A08000] vtkExtractEdges.cxx:435 INFO| \u001b[0mExecuting edge extractor: points are renumbered\u001b[0m\n",
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"\u001b[0m\u001b[2m2022-08-02 20:46:58.680 ( 0.505s) [ E9A08000] vtkExtractEdges.cxx:551 INFO| \u001b[0mCreated 144 edges\u001b[0m\n"
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"model_id": "8833305ed85e4409a9fe2fdec6f65e1c",
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"text": [
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"\u001b[0m\u001b[2m2022-07-15 17:29:58.535 ( 0.659s) [ A689B000] vtkExtractEdges.cxx:435 INFO| \u001b[0mExecuting edge extractor: points are renumbered\u001b[0m\n",
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"\u001b[0m\u001b[2m2022-07-15 17:29:58.536 ( 0.660s) [ A689B000] vtkExtractEdges.cxx:551 INFO| \u001b[0mCreated 144 edges\u001b[0m\n"
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"\u001b[0m\u001b[2m2022-08-02 20:46:58.857 ( 0.682s) [ E9A08000] vtkExtractEdges.cxx:435 INFO| \u001b[0mExecuting edge extractor: points are renumbered\u001b[0m\n",
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"\u001b[0m\u001b[2m2022-08-02 20:46:58.857 ( 0.683s) [ E9A08000] vtkExtractEdges.cxx:551 INFO| \u001b[0mCreated 144 edges\u001b[0m\n"
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"model_id": "279adf14586f46d3a74ff0b59508320e",
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{
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"application/vnd.jupyter.widget-view+json": {
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"model_id": "239cddce9b5c4e09b0c82c36b5f3cac6",
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"model_id": "52757f88d1f94148abb73097db74fbfd",
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‎chapter1/fundamentals_code.py

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# extension: .py
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# format_name: light
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# jupytext_version: 1.13.8
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# jupytext_version: 1.14.1
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# kernelspec:
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# display_name: Python 3 (ipykernel)
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# language: python

‎chapter1/membrane_code.ipynb

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"text": [
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"Info : Meshing 1D...\n",
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"Info : Meshing curve 1 (Ellipse)\n",
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"Info : Done meshing 1D (Wall 0.000842374s, CPU 0.000939s)\n",
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"Info : Done meshing 1D (Wall 0.000226477s, CPU 0.000384s)\n",
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"Info : Meshing 2D...\n",
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"Info : Meshing surface 1 (Plane, Frontal-Delaunay)\n",
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"Info : Done meshing 2D (Wall 0.0902373s, CPU 0.088198s)\n",
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"Info : Done meshing 2D (Wall 0.0965884s, CPU 0.086913s)\n",
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"Info : 1550 nodes 3099 elements\n"
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}
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"outputs": [],
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"source": [
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"Q = fem.FunctionSpace(domain, (\"CG\", 5))\n",
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"expr = fem.Expression(p, Q.element.interpolation_points)\n",
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"expr = fem.Expression(p, Q.element.interpolation_points())\n",
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"pressure = fem.Function(Q)\n",
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"text": [
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"\u001b[0m\u001b[2m2022-07-15 17:30:39.952 ( 0.525s) [ 76AC1000] vtkExtractEdges.cxx:435 INFO| \u001b[0mExecuting edge extractor: points are renumbered\u001b[0m\n",
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"\u001b[0m\u001b[2m2022-07-15 17:30:39.958 ( 0.531s) [ 76AC1000] vtkExtractEdges.cxx:551 INFO| \u001b[0mCreated 4521 edges\u001b[0m\n"
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"\u001b[0m\u001b[2m2022-08-02 20:47:36.095 ( 0.515s) [ AAFB6000] vtkExtractEdges.cxx:435 INFO| \u001b[0mExecuting edge extractor: points are renumbered\u001b[0m\n",
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"\u001b[0m\u001b[2m2022-08-02 20:47:36.097 ( 0.517s) [ AAFB6000] vtkExtractEdges.cxx:551 INFO| \u001b[0mCreated 4521 edges\u001b[0m\n"
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"data": {
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"application/vnd.jupyter.widget-view+json": {
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"model_id": "32d8b1feff23457cb167bf0dc36d7ab8",
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"model_id": "24700d1f20794182a8ddebf1c27e1932",
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"version_major": 2,
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"version_minor": 0
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{
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"data": {
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"application/vnd.jupyter.widget-view+json": {
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"model_id": "1f73d1fd610047b7b68f4ebd6375eec0",
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"model_id": "f8634199f8414d71ae613c7e9874dcbd",
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‎chapter1/membrane_code.py

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# extension: .py
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# jupytext_version: 1.13.8
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# jupytext_version: 1.14.1
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# kernelspec:
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# display_name: Python 3 (ipykernel)
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# We choose a high order function space to represent the function `p`, as it is rapidly varying in space.
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Q = fem.FunctionSpace(domain, ("CG", 5))
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expr = fem.Expression(p, Q.element.interpolation_points)
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expr = fem.Expression(p, Q.element.interpolation_points())
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pressure = fem.Function(Q)
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pressure.interpolate(expr)
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