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Python bindings, segmentation fault, InverseDynamicsFormulationAccForce.data() about tsid HOT 5 CLOSED

stack-of-tasks commented on September 26, 2024

Python bindings, segmentation fault, InverseDynamicsFormulationAccForce.data()

from tsid.

Comments (5)

andreadelprete commented on September 26, 2024

I've tried using the robotpkg version of pinocchio (2.4.3) and I still get the same problem. By debugging python3 I got the following trace:

Thread 1 "python3" received signal SIGSEGV, Segmentation fault.
__memcpy_avx_unaligned () at ../sysdeps/x86_64/multiarch/memcpy-avx-unaligned.S:245
245	../sysdeps/x86_64/multiarch/memcpy-avx-unaligned.S: No such file or directory.
(gdb) where
#0  __memcpy_avx_unaligned () at ../sysdeps/x86_64/multiarch/memcpy-avx-unaligned.S:245
#1  0x00007fffe4f6394e in boost::python::converter::as_to_python_function<pinocchio::DataTpl<double, 0, pinocchio::JointCollectionDefaultTpl>, boost::python::objects::class_cref_wrapper<pinocchio::DataTpl<double, 0, pinocchio::JointCollectionDefaultTpl>, boost::python::objects::make_instance<pinocchio::DataTpl<double, 0, pinocchio::JointCollectionDefaultTpl>, boost::python::objects::value_holder<pinocchio::DataTpl<double, 0, pinocchio::JointCollectionDefaultTpl> > > > >::convert(void const*) () from /opt/openrobots/lib/python3.5/site-packages/pinocchio/libpinocchio_pywrap.so
#2  0x00007fffe0e69f46 in boost::python::detail::caller_arity<1u>::impl<pinocchio::DataTpl<double, 0, pinocchio::JointCollectionDefaultTpl> (*)(tsid::InverseDynamicsFormulationAccForce const&), boost::python::default_call_policies, boost::mpl::vector2<pinocchio::DataTpl<double, 0, pinocchio::JointCollectionDefaultTpl>, tsid::InverseDynamicsFormulationAccForce const&> >::operator()(_object*, _object*) [clone .isra.872] [clone .constprop.1064] ()
   from /home/student/devel/install/lib/python3/dist-packages/tsid/libtsid_pywrap.so
#3  0x00007fffe39f100d in boost::python::objects::function::call(_object*, _object*) const () from /usr/lib/x86_64-linux-gnu/libboost_python-py35.so.1.58.0
#4  0x00007fffe39f1208 in ?? () from /usr/lib/x86_64-linux-gnu/libboost_python-py35.so.1.58.0
#5  0x00007fffe39f9263 in boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const () from /usr/lib/x86_64-linux-gnu/libboost_python-py35.so.1.58.0
#6  0x00007fffe3e5b6d3 in boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<eigenpy::Exception, void (*)(eigenpy::Exception const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(eigenpy::Exception const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) () from /opt/openrobots/lib/libeigenpy.so
#7  0x00007fffe39f901d in boost::python::handle_exception_impl(boost::function0<void>) () from /usr/lib/x86_64-linux-gnu/libboost_python-py35.so.1.58.0
#8  0x00007fffe39ee409 in ?? () from /usr/lib/x86_64-linux-gnu/libboost_python-py35.so.1.58.0
#9  0x00000000005bfd87 in PyObject_Call ()
#10 0x00000000005409bf in PyEval_EvalFrameEx ()
#11 0x0000000000545d8b in PyEval_EvalCodeEx ()
#12 0x00000000004eca18 in ?? ()
#13 0x00000000005bfd87 in PyObject_Call ()
#14 0x00000000004fc63e in ?? ()
#15 0x00000000005bfd87 in PyObject_Call ()
#16 0x00000000005b46a9 in ?? ()
#17 0x0000000000567c9c in ?? ()
#18 0x00000000005bfd87 in PyObject_Call ()
#19 0x00000000005409bf in PyEval_EvalFrameEx ()
#20 0x0000000000544f43 in ?? ()
#21 0x0000000000545c3f in PyEval_EvalCode ()
#22 0x0000000000622642 in ?? ()
#23 0x0000000000624aea in PyRun_FileExFlags ()
#24 0x00000000006252dc in PyRun_SimpleFileExFlags ()
#25 0x000000000063e616 in Py_Main ()
#26 0x00000000004d1761 in main ()

I've tried to ldd the tsid and pinocchio library files and everything looks normal to me:

ldd /opt/openrobots/lib/python3.5/site-packages/pinocchio/libpinocchio_pywrap.so
	linux-vdso.so.1 =>  (0x00007ffe9630e000)
	libeigenpy.so => /opt/openrobots/lib/libeigenpy.so (0x00007f61940ea000)
	libboost_python-py35.so.1.58.0 => /usr/lib/x86_64-linux-gnu/libboost_python-py35.so.1.58.0 (0x00007f6193e9f000)
	libpinocchio.so.2.4.3 => /opt/openrobots/lib/libpinocchio.so.2.4.3 (0x00007f6193c75000)
	libboost_serialization.so.1.58.0 => /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.58.0 (0x00007f6193a14000)
	libboost_system.so.1.58.0 => /usr/lib/x86_64-linux-gnu/libboost_system.so.1.58.0 (0x00007f6193810000)
	liburdfdom_world.so.0.4 => /usr/lib/x86_64-linux-gnu/liburdfdom_world.so.0.4 (0x00007f61935e5000)
	libhpp-fcl.so => /opt/openrobots/lib/libhpp-fcl.so (0x00007f6193184000)
	libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f6192e02000)
	libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f6192af9000)
	libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f61928e3000)
	libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f6192519000)
	libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f61922fc000)
	libboost_filesystem.so.1.58.0 => /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.58.0 (0x00007f61920e4000)
	liburdfdom_model.so.0.4 => /usr/lib/x86_64-linux-gnu/liburdfdom_model.so.0.4 (0x00007f6191eb9000)
	libtinyxml.so.2.6.2 => /usr/lib/x86_64-linux-gnu/libtinyxml.so.2.6.2 (0x00007f6191ca3000)
	libconsole_bridge.so.0.2 => /usr/lib/x86_64-linux-gnu/libconsole_bridge.so.0.2 (0x00007f6191a9e000)
	libassimp.so.3 => /usr/lib/x86_64-linux-gnu/libassimp.so.3 (0x00007f619120f000)
	liboctomap.so.1.9 => /opt/openrobots/lib/liboctomap.so.1.9 (0x00007f6190fa0000)
	liboctomath.so.1.9 => /opt/openrobots/lib/liboctomath.so.1.9 (0x00007f6190d99000)
	/lib64/ld-linux-x86-64.so.2 (0x00007f61959f8000)
	libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f6190b7f000)
	libminizip.so.1 => /usr/lib/x86_64-linux-gnu/libminizip.so.1 (0x00007f6190974000)
student@pinocchiovbox:~/devel/src/tsid/exercizes$ ldd /home/student/devel/install/lib/python3/dist-packages/tsid/libtsid_pywrap.so
	linux-vdso.so.1 =>  (0x00007ffd85f1e000)
	libtsid.so.1.2.3-7-g8eb5 => /home/student/devel/install/lib/libtsid.so.1.2.3-7-g8eb5 (0x00007ff8b8cc2000)
	libboost_python-py35.so.1.58.0 => /usr/lib/x86_64-linux-gnu/libboost_python-py35.so.1.58.0 (0x00007ff8b8a77000)
	libeigenpy.so => /opt/openrobots/lib/libeigenpy.so (0x00007ff8b834c000)
	libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007ff8b7fca000)
	libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007ff8b7db4000)
	libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007ff8b79ea000)
	libboost_system.so.1.58.0 => /usr/lib/x86_64-linux-gnu/libboost_system.so.1.58.0 (0x00007ff8b77e6000)
	libpinocchio.so.2.4.3 => /opt/openrobots/lib/libpinocchio.so.2.4.3 (0x00007ff8b75bc000)
	liburdfdom_world.so.0.4 => /usr/lib/x86_64-linux-gnu/liburdfdom_world.so.0.4 (0x00007ff8b7391000)
	libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007ff8b7088000)
	libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007ff8b6e6b000)
	/lib64/ld-linux-x86-64.so.2 (0x00007ff8b9390000)
	libboost_filesystem.so.1.58.0 => /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.58.0 (0x00007ff8b6c53000)
	liburdfdom_model.so.0.4 => /usr/lib/x86_64-linux-gnu/liburdfdom_model.so.0.4 (0x00007ff8b6a28000)
	libhpp-fcl.so => /opt/openrobots/lib/libhpp-fcl.so (0x00007ff8b65c7000)
	libtinyxml.so.2.6.2 => /usr/lib/x86_64-linux-gnu/libtinyxml.so.2.6.2 (0x00007ff8b63b1000)
	libconsole_bridge.so.0.2 => /usr/lib/x86_64-linux-gnu/libconsole_bridge.so.0.2 (0x00007ff8b61ac000)
	libassimp.so.3 => /usr/lib/x86_64-linux-gnu/libassimp.so.3 (0x00007ff8b591d000)
	liboctomap.so.1.9 => /opt/openrobots/lib/liboctomap.so.1.9 (0x00007ff8b56ae000)
	liboctomath.so.1.9 => /opt/openrobots/lib/liboctomath.so.1.9 (0x00007ff8b54a7000)
	libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007ff8b528d000)
	libminizip.so.1 => /usr/lib/x86_64-linux-gnu/libminizip.so.1 (0x00007ff8b5082000)

from tsid.

andreadelprete commented on September 26, 2024

I've tried using the binary version of TSID (1.2.3r2) and everything works fine.

from tsid.

andreadelprete commented on September 26, 2024

After verifying that the binaries work fine, I have:

uninstalled the binaries of TSID and Pinocchio
checked out the commits of TSID and Pinocchio corresponding to the binaries,
compiled and installed

I still get the same segmentation fault, so it's clearly a problem with my environment. Any idea what it could be?

from tsid.

andreadelprete commented on September 26, 2024

Could this be due to the fact that I have two versions of Eigen?

student@pinocchiovbox:~/devel/src/tsid/exercizes$ dpkg -l | grep eigen
ii  libarpack2                                  3.3.0-1build2                                   amd64        Fortran77 subroutines to solve large scale eigenvalue problems
ii  libeigen3-dev                               3.3~beta1-2                                     all          lightweight C++ template library for linear algebra
ii  robotpkg-eigen-quadprog                     1.0.0r1                                         amd64        QuadProg QP solver using the Eigen3 library
ii  robotpkg-eigen3                             3.3.0                                           amd64        a C++ template library for linear algebra
ii  robotpkg-py35-eigenpy                       2.3.0                                           amd64        Eigen bindings to python
ii  ros-kinetic-eigen-conversions               1.11.9-0xenial-20181107-010715-0800             amd64        Conversion functions between: - Eigen and KDL - Eigen and geometry_msgs.
ii  ros-kinetic-tf2-eigen                       0.5.20-0xenial-20181116-181942-0800             amd64        tf2_eigen

from tsid.

andreadelprete commented on September 26, 2024

Yes, that was the problem. :)
Issue solved!

from tsid.

Related Issues (20)

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ForceTask with moving object HOT 11
GitHub Action HOT 3
Cannot surpress SolverHQuadProg output HOT 3
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undefined symbol error in libtsid_pywrap.so HOT 2
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display error
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build issue with catkin build ROS1 HOT 6
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