Problem while compiling Caribou (VTK) #126

ateixeira0163 · 2022-04-25T11:08:33Z

ateixeira0163
Apr 25, 2022

I'm having problem compiling Caribou.
While doing the command: cmake --build . -j4 I get these messages:

CMake Warning at /home/ateixeira/Sofa/build/install/lib/cmake/SofaEigen2Solver/SofaEigen2SolverConfig.cmake:36 (message):
  SofaEigen2Solver has been removed.  The package still exists for
  compatibility but is empty.  Eigen classes were moved to Sofa.LinearAlgebra
  and SVDLinearSolver to SofaDenseSolver.
Call Stack (most recent call first):
  /home/ateixeira/Sofa/build/install/lib/cmake/SofaBase/SofaBaseConfig.cmake:35 (find_package)
  /home/ateixeira/Sofa/build/install/lib/cmake/SofaGuiCommon/SofaGuiCommonConfig.cmake:34 (find_package)
  /home/ateixeira/Sofa/build/install/lib/cmake/SofaGui/SofaGuiConfig.cmake:37 (find_package)
  /home/ateixeira/Sofa/build/install/plugins/SofaPython3/lib/cmake/SofaPython3/BindingsConfig.cmake:55 (find_package)
  /home/ateixeira/Sofa/build/install/plugins/SofaPython3/lib/cmake/SofaPython3/SofaPython3Config.cmake:86 (include)
  CMakeLists.txt:62 (find_package)


-- Caribou with unittests
-- Caribou with benchmarks
-- Caribou with Python support:
    Version: 3.8.10
    Executable: /usr/bin/python3.8
    Headers: /usr/include/python3.8
    Libraries: /usr/lib/x86_64-linux-gnu/libpython3.8.so
    pybind11 version: 2.4.3
    pybind11 config: /usr/lib/cmake/pybind11/pybind11Config.cmake
-- Caribou with SOFA support
    SOFA version: 21.12.00
    SOFA location: /home/ateixeira/Sofa/build/install
-- Caribou with SofaPython3 support
    SP3 version: 20.12.0
    SP3 location: /home/ateixeira/Sofa/build/install/plugins/SofaPython3
-- Caribou with OpenMP support
	Libraries: /usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so;/usr/lib/x86_64-linux-gnu/libpthread.so
-- Caribou with MKL support
	Include directories: /usr/include/mkl
	Libraries: -Wl,--start-group /usr/lib/x86_64-linux-gnu/libmkl_gf_lp64.a /usr/lib/x86_64-linux-gnu/libmkl_gnu_thread.a /usr/lib/x86_64-linux-gnu/libmkl_core.a -Wl,--end-group;/usr/lib/gcc/x86_64-linux-gnu/10/libgomp.so;/usr/lib/x86_64-linux-gnu/libpthread.so
	Flags: -m64
-- The imported target "vtkParseOGLExt" references the file
   "/usr/bin/vtkParseOGLExt-7.1"
but this file does not exist.  Possible reasons include:
* The file was deleted, renamed, or moved to another location.
* An install or uninstall procedure did not complete successfully.
* The installation package was faulty and contained
   "/usr/lib/cmake/vtk-7.1/VTKTargets.cmake"
but not all the files it references.

-- The imported target "vtkRenderingPythonTkWidgets" references the file
   "/usr/lib/x86_64-linux-gnu/libvtkRenderingPythonTkWidgets.so"
but this file does not exist.  Possible reasons include:
* The file was deleted, renamed, or moved to another location.
* An install or uninstall procedure did not complete successfully.
* The installation package was faulty and contained
   "/usr/lib/cmake/vtk-7.1/VTKTargets.cmake"
but not all the files it references.

-- The imported target "vtk" references the file
   "/usr/bin/vtk"
but this file does not exist.  Possible reasons include:
* The file was deleted, renamed, or moved to another location.
* An install or uninstall procedure did not complete successfully.
* The installation package was faulty and contained
   "/usr/lib/cmake/vtk-7.1/VTKTargets.cmake"
but not all the files it references.

-- The imported target "pvtk" references the file
   "/usr/bin/pvtk"
but this file does not exist.  Possible reasons include:
* The file was deleted, renamed, or moved to another location.
* An install or uninstall procedure did not complete successfully.
* The installation package was faulty and contained
   "/usr/lib/cmake/vtk-7.1/VTKTargets.cmake"
but not all the files it references.

-- Caribou with VTK support
	Include directories: /usr/include/vtk-7.1
	Library directories: /usr//usr/lib/x86_64-linux-gnu
	Libraries directories: vtkCommonCore;vtkCommonDataModel;vtkIOLegacy
	Version: 7.1.1
-- Caribou.Python.Config: /home/ateixeira/Sofa/caribou/build/lib/python3/site-packages/Caribou
-- Caribou.Python.Geometry: /home/ateixeira/Sofa/caribou/build/lib/python3/site-packages/Caribou/Geometry
-- Caribou.Python.Topology: /home/ateixeira/Sofa/caribou/build/lib/python3/site-packages/Caribou/Topology
-- SofaCaribou.Python: /home/ateixeira/Sofa/caribou/build/lib/python3/site-packages/SofaCaribou
-- Configuring done
-- Generating done
-- Build files have been written to: /home/ateixeira/Sofa/caribou/build

And while compiling, I get this error:

[ 33%] Building CXX object unittest/Caribou/Topology/CMakeFiles/Caribou.unittests.Topology.dir/test_vtkreader.cpp.o
In file included from /home/ateixeira/Sofa/caribou/unittest/Caribou/Topology/test_vtkreader.cpp:13:
/home/ateixeira/Sofa/caribou/src/Caribou/Topology/../../Caribou/Topology/IO/VTKReader.h:13:10: fatal error: vtkSmartPointer.h: No such file or directory
   13 | #include <vtkSmartPointer.h>
      |          ^~~~~~~~~~~~~~~~~~~
compilation terminated.
make[2]: *** [unittest/Caribou/Topology/CMakeFiles/Caribou.unittests.Topology.dir/build.make:146: unittest/Caribou/Topology/CMakeFiles/Caribou.unittests.Topology.dir/test_vtkreader.cpp.o] Error 1
make[2]: *** Waiting for unfinished jobs....

I've tried installing libvtk6-dev and python3-vtk7 but with no success.

jnbrunet · 2022-04-26T01:25:06Z

jnbrunet
Apr 26, 2022
Maintainer

Hey @ateixeira0163

Could you try with VTK 9? This is how we install it on our ubuntu 18.04 and 20.04 CI:

$ git clone --depth 1 --branch v9.0.1 https://gitlab.kitware.com/vtk/vtk.git /tmp/vtk
$ cd /tmp/vtk 
$ git submodule update --init 
$ mkdir build && cd build 
$ cmake \
      -GNinja \
      -DCMAKE_C_COMPILER_LAUNCHER=ccache \
      -DCMAKE_CXX_COMPILER_LAUNCHER=ccache \
      -DCMAKE_BUILD_TYPE=Release \
      -DVTK_GROUP_ENABLE_Imaging=NO \
      -DVTK_GROUP_ENABLE_MPI=NO \
      -DVTK_GROUP_ENABLE_Qt=NO \
      -DVTK_GROUP_ENABLE_Rendering=NO \
      -DVTK_GROUP_ENABLE_StandAlone=DEFAULT \
      -DVTK_GROUP_ENABLE_Views=NO \
      -DVTK_GROUP_ENABLE_Web=NO \
      -DVTK_RELOCATABLE_INSTALL=ON \
      -DVTK_MODULE_ENABLE_VTK_IOLegacy=YES \
      -DBUILD_SHARED_LIBS=OFF \
      .. 
$ cmake --build . 
$ cmake --install . 
$ cd /
$ rm -rf /tmp/vtk

If you don't want to install it for the whole system, you can change the installation prefix using the -DCMAKE_INSTALL_PREFIX=/path/to/a/folder cmake option. Then, during Caribou's cmake installation, use the -DVTK_ROOT=/path/to/a/folder cmake option.

Let me know if it helped or not.

4 replies

ateixeira0163 Apr 26, 2022
Author

Hey ! Thanks for the help!!
I tried VTK9 and it worked.
But I got another problem. First, I got the same problem as here: #99
But, after making the changes proposed in it, I got another problem:

>>> import Sofa
---------------------------------------
Checking SOFA_ROOT and SOFAPYTHON3_ROOT
Using environment variable SOFA_ROOT: /home/ateixeira/Sofa/build/
Warning: environment variable SOFAPYTHON3_ROOT is empty. Trying to guess it.
Guessed SOFAPYTHON3_ROOT: /home/ateixeira/Sofa/build
---------------------------------------
>>> import SofaRuntime
>>> import Caribou
>>> import SofaCaribou
[ERROR]   [SofaRuntime] ImportError: generic_type: type "FictitiousGridVec2d" referenced unknown base type "sofa::core::objectmodel::BaseObject"
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/ateixeira/.local/lib/python3.8/site-packages/SofaCaribou/__init__.py", line 6, in <module>
    from .SofaCaribou import *

I've tried to find where the 'FictitiousGridVec2d' is mentioned but I got no success.
Any ideas ? (I'm on 21.12 version of SOFA - last pull on git on 20 January and just pulled from caribou git yesterday)

jnbrunet Apr 27, 2022
Maintainer

Did you compile Caribou out-of-tree? I see that your SOFA_ROOT is set to a build directory. It is usually best practice to put it to your SOFA installation directory (usually build/install if you used the cmake install command without changing the CMAKE_INSTALL_PREFIX variable). Make sure that the compilation of Caribou is also using the installation directory of SOFA. Let me know if that helped.

ateixeira0163 Apr 27, 2022
Author

I've tried this before, but it didn't work. I did a clean compilation of SOFA and Caribou and now its working again!
Just a little extra question, it is possible to use BackwardEulerODESolver to solve Lagragian contacts? Because upon changing the Ode solver from EulerImplicitSolver to BackwardEulerODESolver I get the message :

[ERROR]   [BackwardEulerODESolver(BackwardEulerODESolver)] getSolutionIntegrationFactor not implemented !

jnbrunet Apr 29, 2022
Maintainer

Great !

For the BackwardEulerODESolver, it is unfortunately not compatible. This is on my never ending to do list, see #73

Since Caribou is starting to move a little bit more these last weeks, I might move this issue up in my priorities. I will try to let you know when it is done.

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Problem while compiling Caribou (VTK) #126

ateixeira0163 Apr 25, 2022

Replies: 1 comment · 4 replies

jnbrunet Apr 26, 2022 Maintainer

ateixeira0163 Apr 26, 2022 Author

jnbrunet Apr 27, 2022 Maintainer

ateixeira0163 Apr 27, 2022 Author

jnbrunet Apr 29, 2022 Maintainer

ateixeira0163
Apr 25, 2022

Replies: 1 comment 4 replies

jnbrunet
Apr 26, 2022
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ateixeira0163 Apr 26, 2022
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jnbrunet Apr 27, 2022
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ateixeira0163 Apr 27, 2022
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jnbrunet Apr 29, 2022
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