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Add PyChaste Support for VTK 9 #24

Closed
Tracked by #27
kwabenantim opened this issue Jul 17, 2023 · 9 comments · May be fixed by #72
Closed
Tracked by #27

Add PyChaste Support for VTK 9 #24

kwabenantim opened this issue Jul 17, 2023 · 9 comments · May be fixed by #72
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@kwabenantim @fcooper8472
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enhancement New feature or request
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BBR milestone 3.1

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Description
API changes from VTK 8 to 9: https://vtk.org/Wiki/VTK/API_Changes_8_2_0_to_9_0_0
@kwabenantim kwabenantim self-assigned this Jul 17, 2023
@kwabenantim kwabenantim added the enhancement New feature or request label Jul 17, 2023
@kwabenantim kwabenantim mentioned this issue Jul 22, 2023
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@kwabenantim kwabenantim added this to the BBR milestone 3.1 milestone Sep 19, 2023
@kwabenantim kwabenantim changed the title Support VTK 9 Add PyChaste Support for VTK 9 Nov 14, 2023
@kwabenantim kwabenantim mentioned this issue Nov 14, 2023
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@kwabenantim kwabenantim mentioned this issue Apr 19, 2024
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CMake Error at cmake/Modules/ChasteMacros.cmake:321 (add_library):
  Target "chaste_project_PyChaste" links to target "Freetype::Freetype" but
  the target was not found.  Perhaps a find_package() call is missing for an
  IMPORTED target, or an ALIAS target is missing?
Call Stack (most recent call first):
  cmake/Modules/ChasteMacros.cmake:411 (Chaste_DO_COMMON)
  projects/PyChaste/CMakeLists.txt:65 (chaste_do_project)


CMake Error at cmake/Modules/ChasteMacros.cmake:321 (add_library):
  Target "chaste_project_PyChaste" links to target "X11::X11" but the target
  was not found.  Perhaps a find_package() call is missing for an IMPORTED
  target, or an ALIAS target is missing?
Call Stack (most recent call first):
  cmake/Modules/ChasteMacros.cmake:411 (Chaste_DO_COMMON)
  projects/PyChaste/CMakeLists.txt:65 (chaste_do_project)


CMake Error at cmake/Modules/ChasteMacros.cmake:321 (add_library):
  Target "chaste_project_PyChaste" links to target "GLEW::GLEW" but the
  target was not found.  Perhaps a find_package() call is missing for an
  IMPORTED target, or an ALIAS target is missing?
Call Stack (most recent call first):
  cmake/Modules/ChasteMacros.cmake:411 (Chaste_DO_COMMON)
  projects/PyChaste/CMakeLists.txt:65 (chaste_do_project)


CMake Error at cmake/Modules/ChasteMacros.cmake:321 (add_library):
  Target "chaste_project_PyChaste" links to target "X11::X11" but the target
  was not found.  Perhaps a find_package() call is missing for an IMPORTED
  target, or an ALIAS target is missing?
Call Stack (most recent call first):
  cmake/Modules/ChasteMacros.cmake:411 (Chaste_DO_COMMON)
  projects/PyChaste/CMakeLists.txt:65 (chaste_do_project)


CMake Error at cmake/Modules/ChasteMacros.cmake:321 (add_library):
  Target "chaste_project_PyChaste" links to target "Python3::Module" but the
  target was not found.  Perhaps a find_package() call is missing for an
  IMPORTED target, or an ALIAS target is missing?
Call Stack (most recent call first):
  cmake/Modules/ChasteMacros.cmake:411 (Chaste_DO_COMMON)
  projects/PyChaste/CMakeLists.txt:65 (chaste_do_project)

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kwabenantim commented May 14, 2024 •
edited
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Steps to reproduce the CMake configuration errors:

git clone https://github.com/Chaste/Chaste.git

cd Chaste/projects
git clone --recursive https://github.com/PyChaste/PyChaste.git
cd ..

conda create -n vtk9-env
conda activate vtk9-env
mamba install -c conda-forge -c pychaste boost-cpp hdf5="*=*mpi_mpich*" metis mpich parmetis petsc petsc4py sundials vtk=9 tbb-devel xerces-c xsd xvfbwrapper xorg-libxext six notebook

mkdir build
cd build
export PETSC_DIR=$CONDA_PREFIX
export HDF5_ROOT=$CONDA_PREFIX

cmake \
  -DCMAKE_BUILD_TYPE=Release \
  -DPython3_EXECUTABLE=$(which python) \
  -DCMAKE_LIBRARY_PATH="${CONDA_PREFIX}/lib" \
  -DCMAKE_PREFIX_PATH="${CONDA_PREFIX}" \
  -DCMAKE_INSTALL_PREFIX="${CONDA_PREFIX}" \
  -DBUILD_SHARED_LIBS=ON \
  -DBOOST_ROOT="${CONDA_PREFIX}" \
  -DHDF5_C_COMPILER_EXECUTABLE="${CONDA_PREFIX}/bin/h5pcc" \
  -DVTK_DIR=${CONDA_PREFIX} \
  -DXERCESC_INCLUDE="${CONDA_PREFIX}/include" \
  -DXERCESC_LIBRARY="${CONDA_PREFIX}/lib/libxerces-c.so" \
  -DXSD_EXECUTABLE="${CONDA_PREFIX}/bin/xsd" \
  ..

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@fcooper8472 suggests investigating fixes like those done in https://github.com/Chaste/Chaste/pull/152/files

@kwabenantim kwabenantim mentioned this issue May 14, 2024
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There's now a github action testing this: https://github.com/Chaste/PyChaste/actions/runs/9082771049/job/24959931938

kwabenantim added a commit that referenced this issue May 16, 2024
@kwabenantim
#24 update cmake for vtk9
dda99f6
@kwabenantim kwabenantim mentioned this issue May 16, 2024
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@kwabenantim kwabenantim linked a pull request May 16, 2024 that will close this issue
Support VTK 9 #72
Draft
kwabenantim added a commit that referenced this issue May 16, 2024
@kwabenantim
#24 limit max petsc version
16277fa
kwabenantim added a commit that referenced this issue May 16, 2024
@kwabenantim
#24 restrict max sundials version
5168572
kwabenantim added a commit that referenced this issue May 16, 2024
@kwabenantim
#24 fix vtk components
4f210b4
kwabenantim added a commit that referenced this issue May 16, 2024
@kwabenantim
#24 fix deprecated functions in vtk9
50a52aa
kwabenantim added a commit that referenced this issue May 17, 2024
@kwabenantim
#24 correct p_local_threshold
6433f32
kwabenantim added a commit that referenced this issue May 17, 2024
@kwabenantim
#24 no vtk5 support
e3ff2dc
kwabenantim added a commit that referenced this issue May 17, 2024
@kwabenantim
#24 less verbose vtk smart pointer
6b0201d
kwabenantim added a commit that referenced this issue May 17, 2024
@kwabenantim
#24 less verbose boost shared pointer
f74cb66
kwabenantim added a commit that referenced this issue May 17, 2024
@kwabenantim
#24 restructure cmake
a611e13
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CMake errors are from additional VTK components:

RenderingFreeType # needs Freetype::Freetype
RenderingOpenGL2 # needs X11::X11 and GLEW::GLEW
WrappingPythonCore # needs Python3::Module

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kwabenantim commented May 21, 2024 •
edited
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The errors seem to go away when the extra package modules are searched for directly in Chaste. Possibly subsequent calls to find_package() don't (can't?) add the extra targets correctly?

---find_package(Python3 3.5 )
+++find_package(Python3 3.5 REQUIRED COMPONENTS Interpreter Development)
find_package(
    VTK COMPONENTS CommonCore CommonDataModel FiltersCore FiltersGeneral FiltersGeneric FiltersGeometry
---    FiltersModeling FiltersSources IOCore IOGeometry IOLegacy IOParallelXML IOXML REQUIRED
+++    FiltersModeling FiltersSources IOCore IOGeometry IOLegacy IOParallelXML IOXML
+++    FiltersProgrammable FiltersVerdict InteractionStyle IOImage IOMovie RenderingAnnotation RenderingCore
+++    RenderingFreeType RenderingOpenGL2 WrappingPythonCore  REQUIRED
        )

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kwabenantim commented May 22, 2024 •
edited
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It still works when find_package() is called twice from Chaste to add extra components. Possibly a scope issue? The targets from the first find_package() call seem to disappear after the second call, however.

kwabenantim added a commit that referenced this issue May 22, 2024
@kwabenantim
#24 fix vtkWrappingPythonCore
52dbc06
kwabenantim added a commit that referenced this issue May 22, 2024
@kwabenantim
#24 update cmake
9f85a5d
@kwabenantim
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PyChaste works with VTK9 but needs the cmake find package call to be done above the project scope. This will be done directly in the PyChaste merge into Chaste trunk: Chaste/Chaste#273

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This is now fixed as of Chaste/Chaste@a51678b

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Support VTK 9 Chaste/PyChaste
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@kwabenantim @fcooper8472