Error while compiling SOFA v2012 with Sofapython 3

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  • 29 January 2021 at 01:58 #18417
    nhnhan
    Blocked

    Dear,
    I have tried to compile the newest release of SOFA (v20.12) to play with Sofapython3. Everything looks good until i got this below error:

    FAILED: bin/Bindings.Sofa.Tests 
: && /usr/bin/clang++-11 -Wall -W -Wno-padded -O2 -g -DNDEBUG  applications/plugins/SofaPython3/bindings/Sofa/tests/CMakeFiles/Bindings.Sofa.Tests.dir/PythonModule_Sofa_test.cpp.o applications/plugins/SofaPython3/bindings/Sofa/tests/CMakeFiles/Bindings.Sofa.Tests.dir/Binding_BaseObject_MockComponent.cpp.o -o bin/Bindings.Sofa.Tests  -Wl,-rpath,/home/nhnhanbk/Desktop/sofa/build-v2012/lib::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::  lib/libSofaGTestMain.a  lib/libSofaPython3.so.1.0  lib/libSofaSimulationTree.so.20.12.00  lib/libSofaSimulationGraph.so.20.12.00  lib/libSofaSimulationCommon.so.20.12.00  lib/libSofaSimulationCore.so.20.12.00  lib/libSofaCore.so.20.12.00  lib/libSofaDefaultType.so.20.12.00  lib/libSofaHelper.so.20.12.00  lib/libgtest.so.2.6.2  /usr/lib/x86_64-linux-gnu/libGLU.so  /usr/lib/x86_64-linux-gnu/libGLX.so  /usr/lib/x86_64-linux-gnu/libOpenGL.so  /usr/lib/x86_64-linux-gnu/libGLEW.so  /usr/lib/x86_64-linux-gnu/libboost_system.so  /usr/lib/x86_64-linux-gnu/libboost_filesystem.so  /usr/lib/x86_64-linux-gnu/libboost_program_options.so  /usr/lib/x86_64-linux-gnu/libboost_thread.so  /usr/lib/x86_64-linux-gnu/libboost_chrono.so  /usr/lib/x86_64-linux-gnu/libboost_date_time.so  /usr/lib/x86_64-linux-gnu/libboost_atomic.so  -pthread  /usr/lib/x86_64-linux-gnu/libpython2.7.so  -Wl,-rpath-link,/home/nhnhanbk/Desktop/sofa/build-v2012/lib && :
/usr/bin/ld: lib/libSofaPython3.so.1.0: undefined reference to
_Py_Dealloc'
/usr/bin/ld: lib/libSofaPython3.so.1.0: undefined reference to

    PyUnicode_AsUTF8String’
    /usr/bin/ld: lib/libSofaPython3.so.1.0: undefined reference to `_Py_FalseStruct’
    /usr/bin/ld: lib/libSofaPython3.so.1.0: undefined reference to `PyException_SetTraceback’
    /usr/bin/ld: lib/libSofaPython3.so.1.0: undefined reference to `_PyThreadState_UncheckedGet’
    /usr/bin/ld: lib/libSofaPython3.so.1.0: undefined reference to `PySlice_AdjustIndices’
    /usr/bin/ld: lib/libSofaPython3.so.1.0: undefined reference to `PyUnicode_DecodeUTF8′
    /usr/bin/ld: lib/libSofaPython3.so.1.0: undefined reference to `PyUnicode_FromString’
    /usr/bin/ld: lib/libSofaPython3.so.1.0: undefined reference to `PyThread_tss_set’
    /usr/bin/ld: lib/libSofaPython3.so.1.0: undefined reference to `PyUnicode_FromStringAndSize’
    /usr/bin/ld: lib/libSofaPython3.so.1.0: undefined reference to `PyThread_tss_create’
    /usr/bin/ld: lib/libSofaPython3.so.1.0: undefined reference to `PyBytes_AsString’
    /usr/bin/ld: lib/libSofaPython3.so.1.0: undefined reference to `PyUnicode_DecodeLatin1′
    /usr/bin/ld: lib/libSofaPython3.so.1.0: undefined reference to `PyInstanceMethod_New’
    /usr/bin/ld: lib/libSofaPython3.so.1.0: undefined reference to `PyMem_Calloc’
    /usr/bin/ld: lib/libSofaPython3.so.1.0: undefined reference to `PyBytes_Size’
    /usr/bin/ld: lib/libSofaPython3.so.1.0: undefined reference to `PyThread_tss_get’
    /usr/bin/ld: lib/libSofaPython3.so.1.0: undefined reference to `PyThread_tss_alloc’
    /usr/bin/ld: lib/libSofaPython3.so.1.0: undefined reference to `PyBytes_AsStringAndSize’
    /usr/bin/ld: lib/libSofaPython3.so.1.0: undefined reference to `PyUnicode_AsEncodedString’
    /usr/bin/ld: lib/libSofaPython3.so.1.0: undefined reference to `Py_DecodeLocale’
    /usr/bin/ld: lib/libSofaPython3.so.1.0: undefined reference to `PySlice_Unpack’
    /usr/bin/ld: lib/libSofaPython3.so.1.0: undefined reference to `PyInstanceMethod_Type’
    clang: error: linker command failed with exit code 1 (use -v to see invocation)

    I just wonder that anyone has had this type of error before? or any advice to fix it will be also appreciated. Thank you very much

    1 February 2021 at 10:12 #18452
    jnbrunet
    Moderator

    Hey @nhnhan,

    Did you compile the plugin within the compilation of SOFA or as an out-of-tree plugin? Are you compiling the SofaPython(2) plugin at the same time?

    These errors looks to me as if you are linking against a wrong python version (python 2 maybe?). During the cmake configure stage, it should have a some information on which python version is used for the compilation, something like :

    
$ cmake ..
(...)
-- Python:
    Version: 3.9.1
    Executable: /usr/bin/python3.9
    Headers: /usr/include/python3.9
    Libraries: /usr/lib64/libpython3.9.so
    User site: /home/jnbrunet/.local/lib/python3.9/site-packages
(...)
-- Configuring done
-- Generating done
    10 February 2021 at 05:21 #18562
    PhoNguyen
    Blocked

    Hi,

    I compile sofapython3 with sofa v20.12. There is one error as follows:

    

pho@pho:~/Desktop/plugin.SofaPython3/build$ cmake -DCMAKE_PREFIX_PATH=$SOFA_BLD/install/lib/cmake $SP3_SRC
-- Python:
    Version: 3.9.1
    Executable: /usr/bin/python3.9
    Headers: /usr/include/python3.9
    Libraries: /usr/lib/x86_64-linux-gnu/libpython3.9.so
    User site: /home/pho/.local/lib/python3.9/site-packages
-- pybind11:
    Version: 2.5.0
    Config: /home/pho/anaconda3/share/cmake/pybind11/pybind11Config.cmake
-- SOFA Framework:
	Version: 20.12.00
	Location: /home/pho/Desktop/sofa/build/install
CMake Error at Plugin/CMakeLists.txt:39 (find_package):
  By not providing "FindSofaSimulationGraph.cmake" in CMAKE_MODULE_PATH this
  project has asked CMake to find a package configuration file provided by
  "SofaSimulationGraph", but CMake did not find one.

  Could not find a package configuration file provided by
  "SofaSimulationGraph" with any of the following names:

    SofaSimulationGraphConfig.cmake
    sofasimulationgraph-config.cmake

  Add the installation prefix of "SofaSimulationGraph" to CMAKE_PREFIX_PATH
  or set "SofaSimulationGraph_DIR" to a directory containing one of the above
  files.  If "SofaSimulationGraph" provides a separate development package or
  SDK, be sure it has been installed.

-- Configuring incomplete, errors occurred!

    How can I solve this problem?

    Best,
    Pho

    11 February 2021 at 15:35 #18569
    Guillaume
    Keymaster

    Hi Pho,

    SofaSimulationGraph is now a plugin and is installed in /plugins/SofaSimulationGraph

    In order to be able to find_package plugins, you must add /plugins to CMAKE_PREFIX_PATH.

    Thus, in your case you should do: cmake -DCMAKE_PREFIX_PATH="$SOFA_BLD/install/lib/cmake;$SOFA_BLD/install/plugins" $SP3_SRC

    12 February 2021 at 06:39 #18627
    PhoNguyen
    Blocked

    Hi Guillaume,

    I tried your suggestion, and the errors came as follows:

    
pho@pho:~/Desktop/plugin.SofaPython3/build$ cmake -DCMAKE_PREFIX_PATH="$SOFA_BLD/install/lib/cmake;$SOFA_BLD/install/plugins" $SP3_SRC
CMake Error at CMakeLists.txt:108 (find_package):
  Could not find a package configuration file provided by "pybind11"
  (requested version 2.3) with any of the following names:

    pybind11Config.cmake
    pybind11-config.cmake

  Add the installation prefix of "pybind11" to CMAKE_PREFIX_PATH or set
  "pybind11_DIR" to a directory containing one of the above files.  If
  "pybind11" provides a separate development package or SDK, be sure it has
  been installed.

-- Configuring incomplete, errors occurred!
See also "/home/pho/Desktop/plugin.SofaPython3/SofaPython3/CMakeFiles/CMakeOutput.log".
See also "/home/pho/Desktop/plugin.SofaPython3/SofaPython3/CMakeFiles/CMakeError.log".
pho@pho:~/Desktop/plugin.SofaPython3/build$

    Then I tried to fix this error in Cmake, the error appeared as my previous question.
    How can I solve this problem?

    12 February 2021 at 10:33 #18662
    Hugo
    Keymaster

    Hey @nguyenvanpho

    Have you installed pybind11 as requested in the doc?
    Best

    Hugo

    13 February 2021 at 08:08 #18663
    PhoNguyen
    Blocked

    Hi @Hugo,

    Yeap, I installed pybind11 version 2.5.0 as shown in my question (10 February 2021).

    
-- pybind11:
    Version: 2.5.0
    Config: /home/pho/anaconda3/share/cmake/pybind11/pybind11Config.cmake
-- SOFA Framework:
	Version: 20.12.00
	Location: /home/pho/Desktop/sofa/build/install

    However, when I run this command

    cmake -DCMAKE_PREFIX_PATH="$SOFA_BLD/install/lib/cmake;$SOFA_BLD/install/plugins" $SP3_SRC

    Sofa cannot detect pybind11.

    Best,
    Pho

    13 February 2021 at 15:59 #18664
    jnbrunet
    Moderator

    Hey Pho,

    Something does not seems right here.

    First, concerning your first question, you should not have to add $SOFA_BLD/install/plugins to the cmake prefix path, as this should already be done by the SOFA’s cmake macro. I’m guessing you are on the master branch of SofaPython3, while being on the v20.12 branch of SOFA, since the pluginization of SofaSimulationGraph didn’t make it in the release, hence the cmake error. You need to checkout v20.12 on SofaPython3 as well.

    Next, how is cmake able to output you the version and path of pybind11 if he cannot find it? My guest is that you had previously manually set the cmake path of pybind11 since the latter isn’t installed in a standard path (anaconda) and cmake probably has no idea it exists there.

    Could you try the following:

    
$ cd ~/Desktop/plugin.SofaPython3
$ git checkout v20.12
$ rm -rf build && mkdir build
$ cd build
$ cmake -DCMAKE_PREFIX_PATH="$SOFA_BLD/install/lib/cmake;/home/pho/anaconda3/share" ..

    And let us know how it goes.

    J-N

    14 February 2021 at 03:40 #18665
    PhoNguyen
    Blocked

    Hi @jnbrunet,

    Thank you for your help.
    It is still error:

    
pho@pho:~/Desktop/plugin.SofaPython3/SofaPython3$ git checkout v20.12
Already on 'v20.12'
Your branch is up to date with 'origin/v20.12'.
pho@pho:~/Desktop/plugin.SofaPython3/SofaPython3$ rm -rf build && mkdir build
pho@pho:~/Desktop/plugin.SofaPython3/SofaPython3$ cd build
pho@pho:~/Desktop/plugin.SofaPython3/SofaPython3/build$ cmake -DCMAKE_PREFIX_PATH="$SOFA_BLD/install/lib/cmake;/home/pho/anaconda3/share" ..
CMake Error at CMakeLists.txt:108 (find_package):
  Could not find a package configuration file provided by "pybind11"
  (requested version 2.3) with any of the following names:

    pybind11Config.cmake
    pybind11-config.cmake

  Add the installation prefix of "pybind11" to CMAKE_PREFIX_PATH or set
  "pybind11_DIR" to a directory containing one of the above files.  If
  "pybind11" provides a separate development package or SDK, be sure it has
  been installed.

-- Configuring incomplete, errors occurred!
See also "/home/pho/Desktop/plugin.SofaPython3/SofaPython3/CMakeFiles/CMakeOutput.log".
See also "/home/pho/Desktop/plugin.SofaPython3/SofaPython3/CMakeFiles/CMakeError.log".
pho@pho:~/Desktop/plugin.SofaPython3/SofaPython3/build$
    14 February 2021 at 15:21 #18666
    jnbrunet
    Moderator

    Hi Pho,

    Did you remove your pybind11 previously installed by anaconda? Looks like this file should exists:

    /home/pho/anaconda3/share/cmake/pybind11/pybind11Config.cmake

    Is this still the case?

    In any case, I would suggest you install pybind11 using your system package manager instead of anaconda:

    
# Ubuntu
$ sudo apt install pybind11-dev

# Fedora
$ sudo dnf install pybind11-devel

# MacOS
$ brew install pybind11
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