Pinocchio: Error when building from source (python bindings)

[alejandroastudillo]

Hi,
I have been trying to build pinocchio from source both from the master and devel branches but I haven't succeed. After the make command, I always got the following error:

In file included from /home/alejandro/phd_software/pinocchio_source/pinocchio/build/include/pinocchio/bindings/python/multibody/joint/joints-variant.hpp:11:0,
                 from /home/alejandro/phd_software/pinocchio_source/pinocchio/bindings/python/multibody/joint/expose-joints.cpp:7:
/home/alejandro/phd_software/pinocchio_source/pinocchio/build/include/pinocchio/bindings/python/multibody/joint/joints-models.hpp: In function ‘pinocchio::JointModelComposite& pinocchio::python::addJoint_proxy(pinocchio::JointModelComposite&, const JointModelVariant&, const SE3&)’:
/home/alejandro/phd_software/pinocchio_source/pinocchio/build/include/pinocchio/bindings/python/multibody/joint/joints-models.hpp:79:118: error: call of overloaded ‘apply_visitor(pinocchio::python::JointModelCompositeAddJointVisitor, const JointModelVariant&)’ is ambiguous
       return boost::apply_visitor(JointModelCompositeAddJointVisitor(joint_composite,joint_placement), jmodel_variant);
                                                                                                                      ^

Do you have any idea on what is causing that error?
Thanks in advance

[jcarpent]

On which OS are you working on? If you want, they are some instructions here: https://stack-of-tasks.github.io/pinocchio/download.html

[jcarpent]

By the way, can you provide the complete log of the compilation? It will be easier to identify the compilation error.

[alejandroastudillo]

Sorry for forgetting to mention the OS. I am working on Ubuntu 16.04.
I did succeed with the installation using sudo apt install robotpkg-py27-pinocchio or sudo apt install robotpkg-py35-pinocchio, and have been using pinocchio since some weeks ago. But now, I would like to go for the source builds since I would like to be up to date with the devel branch, or more specifically with the topic/casadi branch from your forked repo @jcarpent.

What I've seen from there is that the only error is the one I already added to my first comment in this issue.
make_output_print.txt

[jcarpent]

Which version of boost are you using now? Because travis is happy when compiling topic/casadi under 16.04. It seems the compilation error is coming from your system set up.
Can you try on a clean 16.04 distribution?

[alejandroastudillo]

These are the versions I am using:

14:37 $ cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/opt/openrobots
-- eigen3 >= 3.0.5 is required.
-- Checking for module 'eigen3 >= 3.0.5'
--   Found eigen3 , version 3.2.92
-- Pkg-config module eigen3 v3.2.92 has been detected with success.
-- urdfdom >= 0.2.0 is required.
-- Checking for module 'urdfdom >= 0.2.0'
--   Found urdfdom , version 0.4.0
-- Pkg-config module urdfdom v0.4.0 has been detected with success.
-- PythonInterp: /usr/bin/python
-- PythonLibraries: /usr/lib/x86_64-linux-gnu/libpython2.7.so
-- PythonLibraryDirs: /usr/lib/x86_64-linux-gnu
-- PythonLibVersionString: 2.7.12
-- Boost version: 1.58.0
-- Boost version: 1.58.0
-- Found the following Boost libraries:
--   filesystem
--   serialization
--   system
--   python
--   unit_test_framework
-- Boost_PYTHON_LIBRARY: /usr/lib/x86_64-linux-gnu/libboost_python.so
-- eigenpy >= 1.4.4 is required.
-- Checking for module 'eigenpy >= 1.4.4'
--   Found eigenpy , version 1.5.1
-- Pkg-config module eigenpy v1.5.1 has been detected with success.
-- Doxygen rendering: using MathJax backend
-- Configuring done
-- Generating done
-- Build files have been written to: /home/alejandro/phd_software/pinocchio_source/pinocchio/build

Can you try on a clean 16.04 distribution?

Not right now, but I will try asap.

BTW, should I remove all robotpkg-* packages before trying to build pinocchio from sources?

[alejandroastudillo]

So, if I try to compile without Python interface (-DBUILD_PYTHON_INTERFACE=OFF), it is able to compile and my C++ examples seem to be working fine. Now, I have turned on the variable BUILD_WITH_CASADI_SUPPORT but cmake is not able to find my version of casadi. Can you tell me what additional command should I use to specify casadi's location? (sorry if this is a stupid question)

[jcarpent]

BTW, should I remove all robotpkg-* packages before trying to build pinocchio from sources?

Yes, otherwise you may have conflicts.

[jcarpent]

So, if I try to compile without Python interface (-DBUILD_PYTHON_INTERFACE=OFF), it is able to compile and my C++ examples seem to be working fine. Now, I have turned on the variable BUILD_WITH_CASADI_SUPPORT but cmake is not able to find my version of casadi. Can you tell me what additional command should I use to specify casadi's location? (sorry if this is a stupid question)

I have opened an issue in CasADi (https://github.com/casadi/casadi/pull/2446), to add the support of pkgconfig. If you install my version (master branch in https://github.com/jcarpent/casadi), you will be able to find casadi with Pinocchio

[alejandroastudillo]

Thanks, I will try with that and see what happens.

[jcarpent]

Any feedback?

[alejandroastudillo]

I tried with casadi supporting pkgconfig, but when building pinocchio, the casadi/casadi.hpp was not found. I added casadi to pinocchio's CMakeLists.txt (using find_library and include_directories) and it is finding casadi now.
The new error is this one:

/home/alejandro/phd_software/pinocchio_source/pinocchio/build/include/pinocchio/math/casadi.hpp:46:16: error: invalid static_cast from type ‘const SX {aka const casadi::Matrix<casadi::SXElem>}’ to type ‘int’
         return static_cast<Scalar>(x);
                ^~~~~~~~~~~~~~~~~~~~~~

BTW, I will be able to try in a clean 16.04 distribution later today or tomorrow.

[jcarpent]

Yes, I would suggest working with a clean Ubuntu environment.
Can you provide me the whole log of the compilation issue (you don't provide the whole information needed to investigate your issue)?

[alejandroastudillo]

I just pulled the updated version of pinocchio from your topic/casadi branch. Here's the whole compilation log.
make_output.txt

The error is shown here:

[jcarpent]

@alejandroastudillo I found the bug which is coming from Eigen in fact. They changed their mind since then. I fixed it in #821. I'm waiting for Travis and it will be merged on devel.

[jcarpent]

This problem has been solved in #821.

[alejandroastudillo]

Thank you very much @jcarpent. I was able to build pinocchio's devel branch from source (haven't tried with python interface). I think that I will test it tomorrow morning and let you know how it goes.

[alejandroastudillo]

Dear @jcarpent. I have been testing the aba algorithm and forward kinematics interfacing casadi. Almost everything is working fine. However, since I need to calculate the casadi expressions which define the pose of a robot's end-effector, I must update the frame placements like this:

pinocchio::forwardKinematics(casadi_model,casadi_data,q_casadi);
pinocchio::updateFramePlacements(casadi_model,casadi_data);

or just: pinocchio::framesForwardKinematics(casadi_model,casadi_data,q_casadi);
taking into account that I already defined:

  typedef double                              Scalar;
  typedef casadi::SX                          CasadiScalar;

  typedef pinocchio::ModelTpl<Scalar>         Model;
  typedef Model::Data                         Data;

  typedef pinocchio::ModelTpl<CasadiScalar>   CasadiModel;
  typedef CasadiModel::Data                   CasadiData;

  ...

  CasadiModel casadi_model = model.cast<CasadiScalar>();
  CasadiData casadi_data(casadi_model);

  ...

  casadi::SX q_sx = casadi::SX::sym("q", model.nq);
  ConfigVectorCasadi q_casadi(model.nq);
  q_casadi = Eigen::Map<ConfigVectorCasadi>(static_cast< std::vector<CasadiScalar> >(q_sx).data(),model.nq,1);

But, whenever I uncomment the pinocchio::updateFramePlacements(casadi_model,casadi_data) call, my script is not compiling.
Both errors are related to the file pinocchio/algorithm/frames.hxx.
The first one is:

/usr/local/include/pinocchio/algorithm/frames.hxx:30:21: error: invalid initialization of reference of type ‘const Frame& {aka const pinocchio::FrameTpl<double>&}’ from expression of type ‘const value_type {aka const pinocchio::FrameTpl<casadi::Matrix<casadi::SXElem>, 0>}’
       const Frame & frame = model.frames[i];
                     ^~~~~

and the second one isrelated to the operator*

/usr/local/include/pinocchio/algorithm/frames.hxx:35:39: error: no match for ‘operator*’ (operand types are ‘__gnu_cxx::__alloc_traits<Eigen::aligned_allocator<pinocchio::SE3Tpl<casadi::Matrix<casadi::SXElem>, 0> > >::value_type {aka pinocchio::SE3Tpl<casadi::Matrix<casadi::SXElem>, 0>}’ and ‘const SE3 {aka const pinocchio::SE3Tpl<double, 0>}’)
         data.oMf[i] = data.oMi[parent]*frame.placement;
                       ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
In file included from /usr/local/include/pinocchio/spatial/se3.hpp:42:0,
                 from /usr/local/include/pinocchio/multibody/model.hpp:10,
                 from /home/alejandro/phd_software/Code/Git_repos/urdf2modelcasadi/urdf2model/src/model_pinocchio/pinocchio_interface.h:8,
                 from /home/alejandro/phd_software/Code/Git_repos/urdf2modelcasadi/urdf2model/src/model_pinocchio/pinocchio_interface.cpp:20:
/usr/local/include/pinocchio/spatial/se3-base.hpp:59:5: note: candidate: typename pinocchio::SE3GroupAction<Derived>::ReturnType pinocchio::SE3Base<Derived>::operator*(const Derived&) const [with Derived = pinocchio::SE3Tpl<casadi::Matrix<casadi::SXElem>, 0>; typename pinocchio::SE3GroupAction<Derived>::ReturnType = pinocchio::SE3Tpl<casadi::Matrix<casadi::SXElem>, 0>]
     operator*(const Derived & m2) const
     ^~~~~~~~
/usr/local/include/pinocchio/spatial/se3-base.hpp:59:5: note:   no known conversion for argument 1 from ‘const SE3 {aka const pinocchio::SE3Tpl<double, 0>}’ to ‘const pinocchio::SE3Tpl<casadi::Matrix<casadi::SXElem>, 0>&’
In file included from /usr/local/include/pinocchio/multibody/joint/joints.hpp:15:0,
                 from /usr/local/include/pinocchio/multibody/joint/joint-collection.hpp:9,
                 from /usr/local/include/pinocchio/multibody/joint/joint-generic.hpp:8,
                 from /usr/local/include/pinocchio/multibody/model.hpp:17,
                 from /home/alejandro/phd_software/Code/Git_repos/urdf2modelcasadi/urdf2model/src/model_pinocchio/pinocchio_interface.h:8,
                 from /home/alejandro/phd_software/Code/Git_repos/urdf2modelcasadi/urdf2model/src/model_pinocchio/pinocchio_interface.cpp:20:
/usr/local/include/pinocchio/multibody/joint/joint-spherical-ZYX.hpp:174:3: note: candidate: template<class Matrix6Like, class S2, int O2> const typename pinocchio::MatrixProduct<typename Eigen::internal::remove_const<typename pinocchio::SizeDepType<3>::ColsReturn<Mat>::ConstType>::type, typename pinocchio::ConstraintSphericalZYXTpl<S2, O2>::Matrix3>::type pinocchio::operator*(const Eigen::MatrixBase<Derived>&, const pinocchio::ConstraintSphericalZYXTpl<S2, O2>&)
   operator*(const Eigen::MatrixBase<Matrix6Like> & Y,
   ^~~~~~~~

.....

Attached there are both the compilation log and my test script.

• frames_compilation_error_log.txt
• test_script.cpp

[jcarpent]

Ok I will have a look and do the appropriate modifications. Thanks for reporting this new issue.

[jcarpent]

@alejandroastudillo I've just made some fixes in #823.

[alejandroastudillo]

Thank you very much @jcarpent. Built, tested, and working.
I'll now try to build with python interface and see what happens.

[alejandroastudillo]

Dear @jcarpent,

Calling cmake with:

cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/opt/openrobots -DBUILD_PYTHON_INTERFACE=ON -DBUILD_WITH_CASADI_SUPPORT=ON

gave me an error related to not finding numpy/numpyconfig.h, but that error was not present when I tried calling cmake with:

cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/opt/openrobots -DBUILD_PYTHON_INTERFACE=ON -DBUILD_WITH_CASADI_SUPPORT=ON  -DPYTHON_INCLUDE_DIR=/usr/include/python2.7 -DPYTHON_LIBRARY=/usr/lib/libpython2.7.so

But now, I am having an error related to the apply_visitor:

In file included from /home/alejandro/phd_software/pinocchio_source/pinocchio/build/include/pinocchio/bindings/python/multibody/joint/joints-variant.hpp:11:0,
                 from /home/alejandro/phd_software/pinocchio_source/pinocchio/bindings/python/multibody/joint/expose-joints.cpp:7:
/home/alejandro/phd_software/pinocchio_source/pinocchio/build/include/pinocchio/bindings/python/multibody/joint/joints-models.hpp: In function ‘pinocchio::JointModelComposite& pinocchio::python::addJoint_proxy(pinocchio::JointModelComposite&, const JointModelVariant&, const SE3&)’:
/home/alejandro/phd_software/pinocchio_source/pinocchio/build/include/pinocchio/bindings/python/multibody/joint/joints-models.hpp:79:118: error: call of overloaded ‘apply_visitor(pinocchio::python::JointModelCompositeAddJointVisitor, const JointModelVariant&)’ is ambiguous
       return boost::apply_visitor(JointModelCompositeAddJointVisitor(joint_composite,joint_placement), jmodel_variant);
                                                                                                                      ^
In file included from /usr/include/boost/variant/apply_visitor.hpp:16:0,
                 from /usr/include/boost/variant/detail/hash_variant.hpp:23,
                 from /usr/include/boost/variant/variant.hpp:34,
                 from /usr/include/boost/variant.hpp:17,
                 from /home/alejandro/phd_software/pinocchio_source/pinocchio/build/include/pinocchio/multibody/joint/joint-collection.hpp:11,
                 from /home/alejandro/phd_software/pinocchio_source/pinocchio/build/include/pinocchio/bindings/python/multibody/joint/joint-derived.hpp:11,
                 from /home/alejandro/phd_software/pinocchio_source/pinocchio/bindings/python/multibody/joint/expose-joints.cpp:6:
/usr/include/boost/variant/detail/apply_visitor_unary.hpp:82:1: note: candidate: typename Visitor::result_type boost::apply_visitor(const Visitor&, Visitable&) [with Visitor = pinocchio::python::JointModelCompositeAddJointVisitor; Visitable = const boost::variant<pinocchio::JointModelRevoluteTpl<double, 0, 0>, pinocchio::JointModelRevoluteTpl<double, 0, 1>, pinocchio::JointModelRevoluteTpl<double, 0, 2>, pinocchio::JointModelFreeFlyerTpl<double, 0>, pinocchio::JointModelPlanarTpl<double, 0>, pinocchio::JointModelRevoluteUnalignedTpl<double, 0>, pinocchio::JointModelSphericalTpl<double, 0>, pinocchio::JointModelSphericalZYXTpl<double, 0>, pinocchio::JointModelPrismaticTpl<double, 0, 0>, pinocchio::JointModelPrismaticTpl<double, 0, 1>, pinocchio::JointModelPrismaticTpl<double, 0, 2>, pinocchio::JointModelPrismaticUnalignedTpl<double, 0>, pinocchio::JointModelTranslationTpl<double, 0>, pinocchio::JointModelRevoluteUnboundedTpl<double, 0, 0>, pinocchio::JointModelRevoluteUnboundedTpl<double, 0, 1>, pinocchio::JointModelRevoluteUnboundedTpl<double, 0, 2>, boost::recursive_wrapper<pinocchio::JointModelCompositeTpl<double, 0, pinocchio::JointCollectionDefaultTpl> > >; typename Visitor::result_type = pinocchio::JointModelCompositeTpl<double>&]
 apply_visitor(const Visitor& visitor, Visitable& visitable)
 ^~~~~~~~~~~~~
/usr/include/boost/variant/detail/apply_visitor_unary.hpp:160:23: note: candidate: decltype(auto) boost::apply_visitor(const Visitor&, Visitable&, typename boost::disable_if<boost::detail::variant::has_result_type<Visitor> >::type*) [with Visitor = pinocchio::python::JointModelCompositeAddJointVisitor; Visitable = const boost::variant<pinocchio::JointModelRevoluteTpl<double, 0, 0>, pinocchio::JointModelRevoluteTpl<double, 0, 1>, pinocchio::JointModelRevoluteTpl<double, 0, 2>, pinocchio::JointModelFreeFlyerTpl<double, 0>, pinocchio::JointModelPlanarTpl<double, 0>, pinocchio::JointModelRevoluteUnalignedTpl<double, 0>, pinocchio::JointModelSphericalTpl<double, 0>, pinocchio::JointModelSphericalZYXTpl<double, 0>, pinocchio::JointModelPrismaticTpl<double, 0, 0>, pinocchio::JointModelPrismaticTpl<double, 0, 1>, pinocchio::JointModelPrismaticTpl<double, 0, 2>, pinocchio::JointModelPrismaticUnalignedTpl<double, 0>, pinocchio::JointModelTranslationTpl<double, 0>, pinocchio::JointModelRevoluteUnboundedTpl<double, 0, 0>, pinocchio::JointModelRevoluteUnboundedTpl<double, 0, 1>, pinocchio::JointModelRevoluteUnboundedTpl<double, 0, 2>, boost::recursive_wrapper<pinocchio::JointModelCompositeTpl<double, 0, pinocchio::JointCollectionDefaultTpl> > >; typename boost::disable_if<boost::detail::variant::has_result_type<Visitor> >::type = void]
 inline decltype(auto) apply_visitor(const Visitor& visitor, Visitable& visitable,
                       ^~~~~~~~~~~~~

The log of this compilation is here: log_compilation.txt

[jcarpent]

A simple question, are you compiling with C++11 or C++14 on? The error coming from /usr/include/boost/variant/detail/apply_visitor_unary.hpp:160 is raised only if flags C++11 or C++14 are activated. @alejandroastudillo Can you check your current configuration?

[alejandroastudillo]

I didn't set any additional flag for C++11 or C++14, but I was using GCC 7.4.0 which needs no flag for enabling C++11 features. I went back to GCC 5.5.0 and now the compilation with python bindings is completed without errors. Thank you very much.

It is worth clarifying that, with GCC 7.4.0, Pinocchio is building without errors only if the python interface is not being built.

[jcarpent]

The issue here is that GCC >= 7.4.0 is complying by default with C++11 enable. Which is not a correct thing (made in the back of users), IMHO. It seems then the problem is coming from Boost 1.58 (on your computer).
In general, I would suggest people relying on the compiler which comes with the distribution, and not to try the most advanced one on an already old Ubuntu distribution (16.04).

@alejandroastudillo Do you think we might close this issue now your problem is solved?

[alejandroastudillo]

Ok. Thank you very much for your advice and help.
Sure, I think this issue can be closed now.