Installation issue
Closed this issue · 14 comments
ddliu365 commented
I tried to install tsid on ubuntu 16.04 and used the devel branch. The error appears while I am using python bindings:
>>> import tsid
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/local/lib/python2.7/dist-packages/tsid/__init__.py", line 1, in <module>
from .libtsid_pywrap import *
ImportError: libeiquadprog.so: cannot open shared object file: No such file or directory
I installed the eiquadprog from the library under stack of tasks.
Is the error caused by lacking of eiquadprog or wrong installation directory as I changed the install directory to cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr/local?
olivier-stasse commented
Dear @ddliugit, thanks for testing TSID.
We are lacking a bit of context.
From your description, it looks like you were able at some point to install eiquadprog on your machine in the
/usr/local
prefix.
If you can verify that /usr/local/lib/libeiquadprog.sois present,
then to me it looks like you are missing
/usr/local/lib
in your LD_LIBRARY_PATH environment variable.
ddliu365 commented
Yes, you are absolutely right.
The problem is fixed after adding the path to the environment variable. However, the tsid cannot be imported since the following error:
import tsid
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/local/lib/python2.7/dist-packages/tsid/__init__.py", line 1, in <module>
from .libtsid_pywrap import *
ImportError: /usr/local/lib/python2.7/dist-packages/tsid/libtsid_pywrap.so: undefined symbol: _ZN7eigenpy9NumpyType4makeEP16tagPyArrayObjectb
andreadelprete commented
Try to update eigenpy with
sudo apt install --reinstall robotpkg-eigenpy
ddliu365 commented
It doesn't work either.
jack@desktop:~$ sudo apt install --reinstall robotpkg-eigenpy
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages were automatically installed and are no longer required:
assimp-utils cython libavdevice-ffmpeg56 libcoin80v5 libcublas7.5
libcudart7.5 libcufft7.5 libcufftw7.5 libcuinj64-7.5 libcurand7.5
libcusolver7.5 libcusparse7.5 libfaad2 libgraphicsmagick-q16-3 libiso9660-8
libmpcdec6 libmysofa0 libnppc7.5 libnppi7.5 libnpps7.5 libnvblas7.5
libnvrtc7.5 libnvtoolsext1 libnvvm3 libopenscenegraph-dev
libopenscenegraph100v5 libopenthreads-dev libopenthreads20 libthrust-dev
libvcdinfo0 libvdpau-dev libx265-179 libx265-188 libxine2 libxine2-bin
libxine2-doc libxine2-ffmpeg libxine2-misc-plugins libxine2-plugins
nvidia-cuda-doc nvidia-cuda-gdb nvidia-opencl-dev nvidia-profiler
nvidia-visual-profiler opencl-headers robotpkg-example-robot-data
robotpkg-hpp-fcl+doc robotpkg-libccd robotpkg-octomap robotpkg-pinocchio
robotpkg-py27-quadprog ros-kinetic-eigenpy
Use 'sudo apt autoremove' to remove them.
0 upgraded, 0 newly installed, 1 reinstalled, 0 to remove and 1 not upgraded.
Need to get 0 B/167 kB of archives.
After this operation, 0 B of additional disk space will be used.
(Reading database ... 415200 files and directories currently installed.)
Preparing to unpack .../robotpkg-eigenpy_1.4.0r2_amd64.deb ...
Unpacking robotpkg-eigenpy (1.4.0r2) over (1.4.0r2) ...
Setting up robotpkg-eigenpy (1.4.0r2) ...
jack@desktop:~$ python
Python 2.7.12 (default, Apr 15 2020, 17:07:12)
[GCC 5.4.0 20160609] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import tsid
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/local/lib/python2.7/dist-packages/tsid/__init__.py", line 1, in <module>
from .libtsid_pywrap import *
ImportError: /usr/local/lib/python2.7/dist-packages/tsid/libtsid_pywrap.so: undefined symbol: _ZN7eigenpy9NumpyType4makeEP16tagPyArrayObjectb
andreadelprete commented
Could you give us the output of this command?
dpkg -l | grep robotpkg
ddliu365 commented
jack@desktop:~/workspace/dg_tutorial_with_turtlesim/src$ dpkg -l | grep robotpkg
ii robotpkg-collada-dom 2.4.0r1 amd64 C++ object representation of a COLLADA XML instance document
ii robotpkg-eigenpy 1.4.0r2 amd64 eigen binding to python
ii robotpkg-example-robot-data 3.4.2 amd64 Robot URDFs for benchmarking and developed examples
ii robotpkg-hpp-fcl+doc 1.4.5 amd64 Humanoid Path Planner (collision detection and distance computations)
ii robotpkg-libccd 2.0 amd64 collision detection
ii robotpkg-octomap 1.9.0 amd64 An Efficient Probabilistic 3D Mapping Framework Based on Octrees
ii robotpkg-openscenegraph 3.6.5r3 amd64 open source high performance 3D graphics toolkit
ii robotpkg-pinocchio 2.4.6 amd64 Efficient rigid body dynamics
ii robotpkg-py27-qt4-gepetto-viewer 4.9.0r1 amd64 Humanoid Path Planner (Simple viewer based on OpenSceneGraph)
ii robotpkg-py27-qt4-gepetto-viewer-corba 5.4.0r2 amd64 Humanoid Path Planner (Corba server for gepetto-viewer)
ii robotpkg-py27-quadprog 0.1.6r1 amd64 Solve a strictly convex quadratic program
ii robotpkg-qt4-osgqt 3.5.7r2 amd64 open source high performance 3D graphics toolkit
andreadelprete commented
Try uninstalling robotpkg-eigenpy and installing instead robotpkg-py27-eigenpy
ddliu365 commented
It doesn't work as I used the robotpkg-py27-eigenpy at the beginning.
jack@desktop:~/repos/mpi_cmake_modules/build$ sudo apt-get remove robotpkg-eigenpy
[sudo] password for jack:
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages were automatically installed and are no longer required:
assimp-utils cython libavdevice-ffmpeg56 libcoin80v5 libcublas7.5
libcudart7.5 libcufft7.5 libcufftw7.5 libcuinj64-7.5 libcurand7.5
libcusolver7.5 libcusparse7.5 libfaad2 libgraphicsmagick-q16-3 libiso9660-8
libmpcdec6 libmysofa0 libnppc7.5 libnppi7.5 libnpps7.5 libnvblas7.5
libnvrtc7.5 libnvtoolsext1 libnvvm3 libopenscenegraph-dev
libopenscenegraph100v5 libopenthreads-dev libopenthreads20 libthrust-dev
libvcdinfo0 libvdpau-dev libx265-179 libx265-188 libxine2 libxine2-bin
libxine2-doc libxine2-ffmpeg libxine2-misc-plugins libxine2-plugins
nvidia-cuda-doc nvidia-cuda-gdb nvidia-opencl-dev nvidia-profiler
nvidia-visual-profiler opencl-headers robotpkg-example-robot-data
robotpkg-hpp-fcl+doc robotpkg-libccd robotpkg-octomap robotpkg-pinocchio
robotpkg-py27-quadprog ros-kinetic-eigenpy
Use 'sudo apt autoremove' to remove them.
The following packages will be REMOVED:
robotpkg-eigenpy
0 upgraded, 0 newly installed, 1 to remove and 1 not upgraded.
After this operation, 0 B of additional disk space will be used.
Do you want to continue? [Y/n] y
(Reading database ... 415199 files and directories currently installed.)
Removing robotpkg-eigenpy (1.4.0r2) ...
jack@desktop:~/repos/mpi_cmake_modules/build$ sudo apt-get install robotpkg-py27-eigenpy
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages were automatically installed and are no longer required:
assimp-utils cython libavdevice-ffmpeg56 libcoin80v5 libcublas7.5
libcudart7.5 libcufft7.5 libcufftw7.5 libcuinj64-7.5 libcurand7.5
libcusolver7.5 libcusparse7.5 libfaad2 libgraphicsmagick-q16-3 libiso9660-8
libmpcdec6 libmysofa0 libnppc7.5 libnppi7.5 libnpps7.5 libnvblas7.5
libnvrtc7.5 libnvtoolsext1 libnvvm3 libopenscenegraph-dev
libopenscenegraph100v5 libopenthreads-dev libopenthreads20 libthrust-dev
libvcdinfo0 libvdpau-dev libx265-179 libx265-188 libxine2 libxine2-bin
libxine2-doc libxine2-ffmpeg libxine2-misc-plugins libxine2-plugins
nvidia-cuda-doc nvidia-cuda-gdb nvidia-opencl-dev nvidia-profiler
nvidia-visual-profiler opencl-headers robotpkg-example-robot-data
robotpkg-hpp-fcl+doc robotpkg-libccd robotpkg-octomap robotpkg-pinocchio
robotpkg-py27-quadprog ros-kinetic-eigenpy
Use 'sudo apt autoremove' to remove them.
The following NEW packages will be installed:
robotpkg-py27-eigenpy
0 upgraded, 1 newly installed, 0 to remove and 1 not upgraded.
Need to get 911 kB of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 http://robotpkg.openrobots.org/packages/debian/pub xenial/robotpkg amd64 robotpkg-py27-eigenpy amd64 2.4.0 [911 kB]
Fetched 911 kB in 2s (432 kB/s)
Selecting previously unselected package robotpkg-py27-eigenpy.
(Reading database ... 415140 files and directories currently installed.)
Preparing to unpack .../robotpkg-py27-eigenpy_2.4.0_amd64.deb ...
Unpacking robotpkg-py27-eigenpy (2.4.0) ...
Setting up robotpkg-py27-eigenpy (2.4.0) ...
jack@desktop:~/repos/mpi_cmake_modules/build$ python
Python 2.7.12 (default, Apr 15 2020, 17:07:12)
[GCC 5.4.0 20160609] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import tsid
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/local/lib/python2.7/dist-packages/tsid/__init__.py", line 1, in <module>
from .libtsid_pywrap import *
ImportError: /usr/local/lib/python2.7/dist-packages/tsid/libtsid_pywrap.so: undefined symbol: _ZN7eigenpy9NumpyType4makeEP16tagPyArrayObjectb
andreadelprete commented
The problem is that you have a too old version of eigenpy. These are the versions of the packages on my machine (same OS as you):
student@pinocchiovbox:~/devel/src/tsid/_build-RELEASE$ dpkg -l | grep robotpkg
ii robotpkg-collada-dom 2.3.1r2 amd64 C++ object representation of a COLLADA XML instance document
ii robotpkg-eiquadprog 1.2.0r1 amd64 algorithm of Goldfarb and Idnani for the solution of a QP
ii robotpkg-hpp-fcl 1.4.4 amd64 Humanoid Path Planner (collision detection and distance computations)
ii robotpkg-libccd 2.0 amd64 collision detection
ii robotpkg-octomap 1.9.0 amd64 An Efficient Probabilistic 3D Mapping Framework Based on Octrees
ii robotpkg-omniorb 4.2.4 amd64 ORB that implements the 2.6 specification of the CORBA
ii robotpkg-osg-dae 3.2.1r2 amd64 DAE module for OSG
ii robotpkg-py35-catkin-pkg 0.4.8 amd64 ROS standalone library for the catkin package
ii robotpkg-py35-eigenpy 2.3.0 amd64 Eigen bindings to python
ii robotpkg-py35-omniorbpy 4.2.4 amd64 Robust high-performance CORBA ORB for Python
ii robotpkg-py35-qt4-gepetto-viewer 4.9.0 amd64 Humanoid Path Planner (Simple viewer based on OpenSceneGraph)
ii robotpkg-py35-qt4-gepetto-viewer-corba 5.4.0 amd64 Humanoid Path Planner (Corba server for gepetto-viewer)
ii robotpkg-py35-quadprog 0.1.6 amd64 Solve a strictly convex quadratic program
ii robotpkg-talos-data 0.0.21r2 amd64 This packages provides data of the humanoid robot Pyrene in a friendly way for the SoT.
ii robotpkg-ur5-description 1.0.1 amd64 Rigid body model of a simple robot arm.
Try executing sudo apt update, then reinstall robotpkg-py27-eigenpy, then recompile TSID from a clean build directory.
ddliu365 commented
Yes, I updated, reinstalled and recompiled. The error still occurred. I am using python 2.7 right now, would that cause any problem?
I think you are using python 3.5
ddliu365 commented
My compiling procedure following pinocchio
cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr/local
make -j4
sudo make install
and then add the following command to the ~/.bashrc
export PATH=/usr/local/bin:$PATH
export PKG_CONFIG_PATH =/usr/local/lib/pkgconfig:$PKG_CONFIG_PATH
export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
export PYTHONPATH =/usr/local/lib/python2.7/site-packages:$PYTHONPATH
andreadelprete commented
Can you execute again dpkg -l | grep robotpkg and tell me the result? Because the problem seemed to be the too old version of eigenpy, so we should know whether that has been fixed by the update.
ddliu365 commented
jack@desktop:~/repos/robot_estimation$ dpkg -l | grep robotpkg
ii robotpkg-collada-dom 2.4.0r1 amd64 C++ object representation of a COLLADA XML instance document
ii robotpkg-example-robot-data 3.4.2 amd64 Robot URDFs for benchmarking and developed examples
ii robotpkg-hpp-fcl+doc 1.4.5 amd64 Humanoid Path Planner (collision detection and distance computations)
ii robotpkg-libccd 2.0 amd64 collision detection
ii robotpkg-octomap 1.9.0 amd64 An Efficient Probabilistic 3D Mapping Framework Based on Octrees
ii robotpkg-openscenegraph 3.6.5r3 amd64 open source high performance 3D graphics toolkit
ii robotpkg-pinocchio 2.4.6 amd64 Efficient rigid body dynamics
ii robotpkg-py27-eigenpy 2.4.0 amd64 Eigen bindings to python
ii robotpkg-py27-qt4-gepetto-viewer 4.9.0r1 amd64 Humanoid Path Planner (Simple viewer based on OpenSceneGraph)
ii robotpkg-py27-qt4-gepetto-viewer-corba 5.4.0r2 amd64 Humanoid Path Planner (Corba server for gepetto-viewer)
ii robotpkg-py27-quadprog 0.1.6r1 amd64 Solve a strictly convex quadratic program
ii robotpkg-qt4-osgqt 3.5.7r2 amd64 open source high performance 3D graphics toolkit
ddliu365 commented
The problem is solved!
Thanks for your help!