Import Error while importing Pinocchio #2081

threedee003 · 2023-11-09T11:51:09Z

threedee003
Nov 9, 2023

Dear @jorisv,
I am trying to install Pinocchio in the latest Isaac Sim 2023.1.0 python version so that I can use it for robotic simulation applications. But however I am getting the following import error.
ISAAC_SIM_23 is the python.sh file provided by Nvidia.

I installed Pinocchio using ISAAC_SIM_23 -m pip install pin

This is the error message from the terminal.

bikram@01hw1695605:~/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/standalone_examples/api/omni.isaac.husky_ur3_robotiq/IK-utils$ ISAAC_SIM_23 
Python 3.10.13 (main, Sep  6 2023, 19:28:27) [GCC 7.3.1 20180303 (Red Hat 7.3.1-5)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pinocchio
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/bikram/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/python/lib/python3.10/site-packages/cmeel.prefix/lib/python3.10/site-packages/pinocchio/__init__.py", line 6, in <module>
    from .pinocchio_pywrap import *
ImportError: /usr/lib/x86_64-linux-gnu/libboost_python38.so.1.71.0: undefined symbol: _Py_fopen
>>>

Can you please tell me how can I fix this or what should I do ?

Thanks and regards,
Tribikram.

Answered by nim65s

Nov 14, 2023

you are able to use pip for pinocchio as long as you are not simultaneously trying to use binaries from ROS apt packages.
I guess you update some environment variables or source a /opt/ros/noetic/setup.sh file in your ~/.bashrc. Remove this from your bashrc, open a new shell, and you're good to go.

Alternatively, just run export LD_LIBRARY_PATH="" in a shell, and after that you can use pip for pinocchio in that shell.

View full answer

nim65s · 2023-11-09T12:22:56Z

nim65s
Nov 9, 2023
Maintainer

Hi @threedee003,

This shouldn't link to boost python 1.71 from the system, but from boost python 1.82 from pip.

Could you show us the result of the env command and also ldd /home/bikram/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/python/lib/python3.10/site-packages/cmeel.prefix/lib/python3.10/site-packages/pinocchio/pinocchio_pywrap*.so ?

4 replies

threedee003 Nov 10, 2023
Author

Hello @nim65s ,
Here you go

bikram@01hw1695605:~$ env
SHELL=/bin/bash
ROS_VERSION=1
SESSION_MANAGER=local/01hw1695605:@/tmp/.ICE-unix/4629,unix/01hw1695605:/tmp/.ICE-unix/4629
QT_ACCESSIBILITY=1
COLORTERM=truecolor
XDG_CONFIG_DIRS=/etc/xdg/xdg-ubuntu:/etc/xdg
XDG_MENU_PREFIX=gnome-
GNOME_DESKTOP_SESSION_ID=this-is-deprecated
CONDA_EXE=/home/bikram/anaconda3/bin/conda
_CE_M=
PKG_CONFIG_PATH=/home/bikram/husky_ws/devel/lib/pkgconfig:/opt/ros/noetic/lib/pkgconfig:/opt/ros/noetic/lib/x86_64-linux-gnu/pkgconfig
ROS_PYTHON_VERSION=3
TERMINATOR_DBUS_PATH=/net/tenshu/Terminator2
GNOME_SHELL_SESSION_MODE=ubuntu
SSH_AUTH_SOCK=/run/user/1003/keyring/ssh
TERMINATOR_UUID=urn:uuid:6324070e-bfd9-4c7c-aad5-1673c1c92688
XMODIFIERS=@im=ibus
DESKTOP_SESSION=ubuntu
SSH_AGENT_PID=4594
ROS_PACKAGE_PATH=/home/bikram/ur3_husky_ws/src:/home/bikram/husky_ws/src:/opt/ros/noetic/share
GTK_MODULES=gail:atk-bridge
ROSLISP_PACKAGE_DIRECTORIES=/home/bikram/husky_ws/devel/share/common-lisp
PWD=/home/bikram
LOGNAME=bikram
XDG_SESSION_DESKTOP=ubuntu
XDG_SESSION_TYPE=x11
GPG_AGENT_INFO=/run/user/1003/gnupg/S.gpg-agent:0:1
XAUTHORITY=/run/user/1003/gdm/Xauthority
WINDOWPATH=2
HOME=/home/bikram
USERNAME=bikram
IM_CONFIG_PHASE=1
LANG=en_IN
DESKTOP_MODE=1
ROS_ETC_DIR=/opt/ros/noetic/etc/ros
LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.zst=01;31:*.tzst=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.wim=01;31:*.swm=01;31:*.dwm=01;31:*.esd=01;31:*.jpg=01;35:*.jpeg=01;35:*.mjpg=01;35:*.mjpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.m4a=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.oga=00;36:*.opus=00;36:*.spx=00;36:*.xspf=00;36:
XDG_CURRENT_DESKTOP=ubuntu:GNOME
VTE_VERSION=6003
CMAKE_PREFIX_PATH=/home/bikram/husky_ws/devel:/opt/ros/noetic
INVOCATION_ID=0b5c5b9164884a3b84ffbb3b8e201196
TERMINATOR_DBUS_NAME=net.tenshu.Terminator23558193cd9818af7fe4d2c2f5bd9d00f
MANAGERPID=4419
LESSCLOSE=/usr/bin/lesspipe %s %s
XDG_SESSION_CLASS=user
PYTHONPATH=/home/bikram/.local/share/ov/pkg/isaac_sim-2022.2.1/exts/omni.isaac.core/omni/isaac/core:/home/bikram/.local/share/ov/pkg/isaac_sim-2022.2.1/exts/omni.isaac.examples:/home/bikram/.local/share/ov/pkg/isaac_sim-*/python.sh:/home/bikram/husky_ws/devel/lib/python3/dist-packages:/opt/ros/noetic/lib/python3/dist-packages
TERM=xterm-256color
_CE_CONDA=
LESSOPEN=| /usr/bin/lesspipe %s
USER=bikram
CONDA_SHLVL=0
DISPLAY=:1
SHLVL=1
ROS_MASTER_URI=http://localhost:11311
QT_IM_MODULE=ibus
ENSENSO_INSTALL=/opt/ensenso
CONDA_PYTHON_EXE=/home/bikram/anaconda3/bin/python
LD_LIBRARY_PATH=/home/bikram/husky_ws/devel/lib:/opt/ros/noetic/lib:/opt/ros/noetic/lib/x86_64-linux-gnu
XDG_RUNTIME_DIR=/run/user/1003
JOURNAL_STREAM=8:49815
XDG_DATA_DIRS=/usr/share/ubuntu:/usr/local/share/:/usr/share/:/var/lib/snapd/desktop
PATH=/home/bikram/anaconda3/condabin:/opt/ros/noetic/bin:/home/bikram/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
GDMSESSION=ubuntu
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/1003/bus
ROS_ROOT=/opt/ros/noetic/share/ros
ROS_DISTRO=noetic
GIO_LAUNCHED_DESKTOP_FILE_PID=78149
_=/usr/bin/env

and


bikram@01hw1695605:~$ ldd /home/bikram/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/python/lib/python3.10/site-packages/cmeel.prefix/lib/python3.10/site-packages/pinocchio/pinocchio_pywrap*.so
	linux-vdso.so.1 (0x00007ffee5984000)
	libeigenpy.so => /opt/ros/noetic/lib/x86_64-linux-gnu/libeigenpy.so (0x00007fa295871000)
	libpinocchio.so => /home/bikram/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/python/lib/python3.10/site-packages/cmeel.prefix/lib/python3.10/site-packages/pinocchio/../../../../lib/libpinocchio.so (0x00007fa29583b000)
	libboost_python310.so.1.82.0 => /home/bikram/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/python/lib/python3.10/site-packages/cmeel.prefix/lib/python3.10/site-packages/pinocchio/../../../../lib/libboost_python310.so.1.82.0 (0x00007fa2957fe000)
	libboost_filesystem.so.1.82.0 => /home/bikram/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/python/lib/python3.10/site-packages/cmeel.prefix/lib/python3.10/site-packages/pinocchio/../../../../lib/libboost_filesystem.so.1.82.0 (0x00007fa2957da000)
	libboost_system.so.1.82.0 => /home/bikram/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/python/lib/python3.10/site-packages/cmeel.prefix/lib/python3.10/site-packages/pinocchio/../../../../lib/libboost_system.so.1.82.0 (0x00007fa2957d3000)
	liburdfdom_sensor.so.3.0 => /home/bikram/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/python/lib/python3.10/site-packages/cmeel.prefix/lib/python3.10/site-packages/pinocchio/../../../../lib/liburdfdom_sensor.so.3.0 (0x00007fa2957c8000)
	liburdfdom_model.so.3.0 => /home/bikram/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/python/lib/python3.10/site-packages/cmeel.prefix/lib/python3.10/site-packages/pinocchio/../../../../lib/liburdfdom_model.so.3.0 (0x00007fa29579c000)
	liburdfdom_world.so.3.0 => /home/bikram/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/python/lib/python3.10/site-packages/cmeel.prefix/lib/python3.10/site-packages/pinocchio/../../../../lib/liburdfdom_world.so.3.0 (0x00007fa295770000)
	libconsole_bridge.so.1.0 => /home/bikram/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/python/lib/python3.10/site-packages/cmeel.prefix/lib/python3.10/site-packages/pinocchio/../../../../lib/libconsole_bridge.so.1.0 (0x00007fa295769000)
	libtinyxml.so => /home/bikram/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/python/lib/python3.10/site-packages/cmeel.prefix/lib/python3.10/site-packages/pinocchio/../../../../lib/libtinyxml.so (0x00007fa29574f000)
	libhpp-fcl.so => /home/bikram/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/python/lib/python3.10/site-packages/cmeel.prefix/lib/python3.10/site-packages/pinocchio/../../../../lib/libhpp-fcl.so (0x00007fa29543a000)
	libboost_serialization.so.1.82.0 => /home/bikram/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/python/lib/python3.10/site-packages/cmeel.prefix/lib/python3.10/site-packages/pinocchio/../../../../lib/libboost_serialization.so.1.82.0 (0x00007fa2953f4000)
	libboost_chrono.so.1.82.0 => /home/bikram/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/python/lib/python3.10/site-packages/cmeel.prefix/lib/python3.10/site-packages/pinocchio/../../../../lib/libboost_chrono.so.1.82.0 (0x00007fa2953ea000)
	liboctomap.so => /opt/ros/noetic/lib/liboctomap.so (0x00007fa2953a1000)
	liboctomath.so => /opt/ros/noetic/lib/liboctomath.so (0x00007fa295397000)
	libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007fa29516d000)
	libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fa29501e000)
	libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007fa295003000)
	libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fa294e11000)
	libboost_python38.so.1.71.0 => /usr/lib/x86_64-linux-gnu/libboost_python38.so.1.71.0 (0x00007fa294dd0000)
	librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007fa294dc4000)
	libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007fa294dbe000)
	libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007fa294d9b000)
	libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x00007fa294d96000)
	libboost_atomic.so.1.82.0 => /home/bikram/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/python/lib/python3.10/site-packages/cmeel.prefix/lib/python3.10/site-packages/pinocchio/../../../../lib/libboost_atomic.so.1.82.0 (0x00007fa294d8c000)
	libassimp.so.5 => /home/bikram/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/python/lib/python3.10/site-packages/cmeel.prefix/lib/python3.10/site-packages/pinocchio/../../../../lib/libassimp.so.5 (0x00007fa294334000)
	/lib64/ld-linux-x86-64.so.2 (0x00007fa297506000)
	libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007fa294318000)

nim65s Nov 10, 2023
Maintainer

Ok, then your issue here is that you are mixing 2 packages managers: apt for ROS and pip for pinocchio. I'd suggest to choose only one, by either deactivating your ROS environment and using only pip, or by installing pinocchio from ROS instead of installing it from pip.

The workaround on your current state is export LD_LIBRARY_PATH=""

threedee003 Nov 10, 2023
Author

@nim65s
I am new to Linux. I was a Windows user :")
Can you tell me how to use the pip for pinocchio ?

nim65s Nov 14, 2023
Maintainer

you are able to use pip for pinocchio as long as you are not simultaneously trying to use binaries from ROS apt packages.
I guess you update some environment variables or source a /opt/ros/noetic/setup.sh file in your ~/.bashrc. Remove this from your bashrc, open a new shell, and you're good to go.

Alternatively, just run export LD_LIBRARY_PATH="" in a shell, and after that you can use pip for pinocchio in that shell.

Answer selected by threedee003

BoxingWing · 2023-11-19T09:37:30Z

BoxingWing
Nov 19, 2023

Hello guys. I also tried to install Pinocchio into the embedded Python of Isaac Sim. Similar to @threedee003 , I use ./python.sh -m pip install pin to install Pinocchio, where python.sh is provided by Isaac Sim. The installation is successful:

boxing@boxing-ASUS--Laptop:~/Desktop$ ISAACSIM_PYTHON -m pip install pin
Collecting pin
  Using cached pin-2.6.20-1-cp310-cp310-manylinux_2_28_x86_64.whl (6.1 MB)
Requirement already satisfied: cmeel-tinyxml<3,>=2.6.2.2 in /home/boxing/.local/lib/python3.10/site-packages (from pin) (2.6.2.2)
Requirement already satisfied: cmeel-console-bridge<2,>=1.0.2.2 in /home/boxing/.local/lib/python3.10/site-packages (from pin) (1.0.2.2)
Requirement already satisfied: cmeel-urdfdom<4,>=3.1.0.3 in /home/boxing/.local/lib/python3.10/site-packages (from pin) (3.1.0.3)
Requirement already satisfied: cmeel-boost~=1.82.0 in /home/boxing/.local/lib/python3.10/site-packages (from pin) (1.82.0)
Requirement already satisfied: cmeel in /home/boxing/.local/lib/python3.10/site-packages (from pin) (0.51.1)
Requirement already satisfied: hpp-fcl<4,>=2.3.4 in /home/boxing/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/python/lib/python3.10/site-packages (from pin) (2.3.6)
Requirement already satisfied: numpy<1.25,>=1.23 in /home/boxing/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/exts/omni.kit.pip_archive/pip_prebundle (from cmeel-boost~=1.82.0->pin) (1.23.5)
Requirement already satisfied: cmeel-assimp<6,>=5.2.5.1 in /home/boxing/.local/lib/python3.10/site-packages (from hpp-fcl<4,>=2.3.4->pin) (5.2.5.1)
Requirement already satisfied: eigenpy<4,>=3.1 in /home/boxing/.local/lib/python3.10/site-packages (from hpp-fcl<4,>=2.3.4->pin) (3.1.3)
Requirement already satisfied: cmeel-octomap<2,>=1.9.8.2 in /home/boxing/.local/lib/python3.10/site-packages (from hpp-fcl<4,>=2.3.4->pin) (1.9.8.2)
Requirement already satisfied: tomli<3.0.0,>=2.0.1 in /home/boxing/.local/lib/python3.10/site-packages (from cmeel->pin) (2.0.1)
Installing collected packages: pin
Successfully installed pin-2.6.20
WARNING: You are using pip version 21.2.1+nv1; however, version 23.3.1 is available.
You should consider upgrading via the '/home/boxing/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/python/bin/python3 -m pip install --upgrade pip' command.

The weird thing is that when I try to import Pinocchio, the Isaac Sim's python interpreter gives me a ModuleNotFoundError:

boxing@boxing-ASUS--Laptop:~/Desktop$ ISAACSIM_PYTHON 
Python 3.10.13 (main, Sep  6 2023, 19:28:27) [GCC 7.3.1 20180303 (Red Hat 7.3.1-5)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pinocchio
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ModuleNotFoundError: No module named 'pinocchio'

May I have some suggestions?

5 replies

nim65s Nov 19, 2023
Maintainer

Could you provide the output of ISAACSIM_PYTHON -c "import sys; print(sys.path)" ?

BoxingWing Nov 20, 2023

Sure.

boxing@boxing-ASUS--Laptop:~/Desktop$ ISAACSIM_PYTHON 
Python 3.10.13 (main, Sep  6 2023, 19:28:27) [GCC 7.3.1 20180303 (Red Hat 7.3.1-5)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import sys
>>> for i in sys.path:\
... print(i)   
... 

/home/boxing/Desktop
/home/boxing/.local/share
/home/boxing/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/exts/omni.isaac.kit
/home/boxing/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/exts/omni.isaac.gym
/home/boxing/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/kernel/py
/home/boxing/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/plugins/bindings-python
/home/boxing/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/exts/omni.isaac.lula/pip_prebundle
/home/boxing/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/exts/omni.exporter.urdf/pip_prebundle
/home/boxing/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/exts/omni.kit.pip_archive/pip_prebundle
/home/boxing/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/exts/omni.isaac.core_archive/pip_prebundle
/home/boxing/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/exts/omni.isaac.ml_archive/pip_prebundle
/home/boxing/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/exts/omni.pip.compute/pip_prebundle
/home/boxing/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/exts/omni.pip.cloud/pip_prebundle
/home/boxing/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/extscache/omni.pip.torch-2_0_1-2.0.2+105.1.lx64/torch-2-0-1
/home/boxing/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/python/lib/python310.zip
/home/boxing/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/python/lib/python3.10
/home/boxing/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/python/lib/python3.10/lib-dynload
/home/boxing/.local/lib/python3.10/site-packages
/home/boxing/.local/lib/python3.10/site-packages/cmeel.prefix/lib/python3.10/site-packages
/home/boxing/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/python/lib/python3.10/site-packages

I also did some other explorations, hoping they might be of some use:

check the python interpreter:

boxing@boxing-ASUS--Laptop:~$ ISAACSIM_PYTHON
Python 3.10.13 (main, Sep  6 2023, 19:28:27) [GCC 7.3.1 20180303 (Red Hat 7.3.1-5)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import sys
>>> sys.executable
'/home/boxing/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/python/bin/python3'

check the pinocchio package:

boxing@boxing-ASUS--Laptop:~/Desktop$ ISAACSIM_PYTHON -m pip show pin
Name: pin
Version: 2.6.20
Summary: A fast and flexible implementation of Rigid Body Dynamics algorithms and their analytical derivatives
Home-page: https://github.com/stack-of-tasks/pinocchio
Author: 
Author-email: 
License: 
Location: /home/boxing/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/python/lib/python3.10/site-packages
Requires: cmeel-boost, cmeel-tinyxml, cmeel, cmeel-urdfdom, hpp-fcl, cmeel-console-bridge
Required-by:

check the installed directory of Pinocchio:

boxing@boxing-ASUS--Laptop:~/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/python/lib/python3.10/site-packages$ ls
cmeel                                   cmeel_tinyxml-2.6.2.2.dist-info  numpy-1.24.4.dist-info    setuptools
cmeel-0.51.1.dist-info                  cmeel_urdfdom-3.1.1.dist-info    numpy.libs                setuptools-65.5.1.dist-info
cmeel_assimp-5.3.1.dist-info            _distutils_hack                  pin-2.6.20.dist-info      tomli
cmeel_boost-1.82.0.dist-info            distutils-precedence.pth         pip                       tomli-2.0.1.dist-info
cmeel_console_bridge-1.0.2.2.dist-info  eigenpy-3.1.3.dist-info          pip-21.2.1+nv1.dist-info
cmeel_octomap-1.9.8.2.dist-info         hpp_fcl-2.3.6.dist-info          pkg_resources
cmeel.prefix                            numpy                            README.txt
boxing@boxing-ASUS--Laptop:~/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/python/lib/python3.10/site-packages$ cd pin-2.6.20.dist-info/
boxing@boxing-ASUS--Laptop:~/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/python/lib/python3.10/site-packages/pin-2.6.20.dist-info$ ls
INSTALLER  license  METADATA  RECORD  REQUESTED  top_level.txt  WHEEL

BoxingWing Nov 20, 2023

Hi, Guilhem @nim65s, some updates here. I have installed Pinocchio via robotpkg, and configured environment variables as instructed at https://stack-of-tasks.github.io/pinocchio/download.html. Now if I try ISAACSIM_PYTHON -c "import pinocchio", there will be no errors. Note that ISAACSIM_PYTHON points to a python.sh file in the root folder of Isaac Sim.

I'm sorry to say that another problem shows up. After I start the Isaac Sim GUI app, open the embedded python script editor
from the GUI, try to test some codes, it still cannot find the Pinocchio module. I mannuly add the search path via sys.path.append(), then the error becomes an import error relates to libhpp-fcl.so. Here are the codes and results:

CODES:
import sys
sys.path.append("/opt/openrobots/bin")
sys.path.append("/opt/openrobots/lib")
sys.path.append("/opt/openrobots/lib/pkgconfig")
sys.path.append("/opt/openrobots/lib/python3.10/site-packages")
for i in sys.path:
	print(i)
import pinocchio

RESULTS:
/home/boxing/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/python/lib/python310.zip
/home/boxing/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/python/lib/python3.10
/home/boxing/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/python/lib/python3.10/lib-dynload
/home/boxing/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/python/lib/python3.10/site-packages
.
/home/boxing/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/kernel/py
/home/boxing/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/plugins/bindings-python
/home/boxing/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/bindings-python
/home/boxing/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/scripting-python-3.10/libs
/home/boxing/.local/share/ov/data/Kit/Isaac-Sim/2023.1/pip3-envs/default
<PATH_TO_noetic_ws>/devel/lib/python3/dist-packages/isaac_tutorials/msg
/opt/openrobots/bin
/opt/openrobots/lib
/opt/openrobots/lib/pkgconfig
/opt/openrobots/lib/python3.10/site-packages
2023-11-20 06:28:16 [48,692ms] [Error] [carb.scripting-python.plugin] ImportError: /opt/openrobots/lib/libhpp-fcl.so: undefined symbol: _ZNK6Assimp8IOSystem16CurrentDirectoryB5cxx11Ev

At:
  /opt/openrobots/lib/python3.10/site-packages/pinocchio/__init__.py(6): <module>
  <frozen importlib._bootstrap>(241): _call_with_frames_removed
  <frozen importlib._bootstrap_external>(883): exec_module
  <frozen importlib._bootstrap>(703): _load_unlocked
  <frozen importlib._bootstrap>(1006): _find_and_load_unlocked
  <frozen importlib._bootstrap>(1027): _find_and_load
  /tmp/carb.grV05v/script_1700461696.py(10): <module>

I guess the Isaac Sim app starts a different python interpreter? Or maybe it blocks something after it starts? Is there anything we can do about this problem?

nim65s Nov 20, 2023
Maintainer

I would expect isaac sim to start a different python interpreter, and in that case installing apt packages from robotpkg shouldn't help, and could break stuff. I'd suggest uninstalling this and removing /opt/openrobots mentions in your environment.

your ls in ~/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/python/lib/python3.10/site-package show the issue. there is no pinocchio folder, or cmeel.pth file to make python look into ~/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/python/lib/python3.10/site-package/cmeel.prefix/lib/python3.10/site-package.

I can also see multiple references about /home/boxing/.local/lib/python3.10/site-packages, which might get mixed in a bad way with stuff installed by the python interpreter of your system, but I'm not sure.

I don't really understand what isaac sim python is doing. It looks like it installed pinocchio in ov/pkg while putting all its dependencies in another prefix.

Maybe we can try to use a virtual environment, to properly isolate and install what we need ?
Something like ISAACSIM_PYTHON -m venv ~/my-pin-venv && source ~/my-pin-venv/bin/activate && pip install pin && python -c "import pinocchio" maybe.

BoxingWing Nov 21, 2023

Hi, I have removed the /opt/openrobots mentions and tried the virtual emvironment. python -c import pinocchio gives no error. But again, after I enter the Isaac sim app, the import error shows up again in the embedded python script editor.

Here's what I got out of Isaac sim:

(my-pin-venv) boxing@boxing-ASUS--Laptop:~$ python
Python 3.10.13 (main, Sep  6 2023, 19:28:27) [GCC 7.3.1 20180303 (Red Hat 7.3.1-5)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import sys
>>> for i in sys.path:\
... print(i)
... 

/home/boxing/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/python/lib/python310.zip
/home/boxing/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/python/lib/python3.10
/home/boxing/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/python/lib/python3.10/lib-dynload
/home/boxing/my-pin-venv/lib/python3.10/site-packages
/home/boxing/my-pin-venv/lib/python3.10/site-packages/cmeel.prefix/lib/python3.10/site-packages
>>> import pinocchio
>>> pinocchio.__file__
'/home/boxing/my-pin-venv/lib/python3.10/site-packages/cmeel.prefix/lib/python3.10/site-packages/pinocchio/__init__.py'

Here's what I got inside the Isaac Sim:

CODES:
import sys
print(sys.executable)
for i in sys.path:
	print(i)
import pinocchio

RESULTS:
/home/boxing/my-pin-venv/bin/python3
/home/boxing/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/python/lib/python310.zip
/home/boxing/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/python/lib/python3.10
/home/boxing/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/python/lib/python3.10/lib-dynload
/home/boxing/my-pin-venv/lib/python3.10/site-packages
/home/boxing/my-pin-venv/lib/python3.10/site-packages/cmeel.prefix/lib/python3.10/site-packages
.
/home/boxing/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/kernel/py
/home/boxing/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/plugins/bindings-python
/home/boxing/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/bindings-python
/home/boxing/.local/share/ov/pkg/isaac_sim-2023.1.0-hotfix.1/kit/scripting-python-3.10/libs
/home/boxing/.local/share/ov/data/Kit/Isaac-Sim/2023.1/pip3-envs/default
2023-11-21 01:40:49 [142,415ms] [Error] [carb.scripting-python.plugin] ImportError: /home/boxing/my-pin-venv/lib/python3.10/site-packages/cmeel.prefix/lib/python3.10/site-packages/pinocchio/../../../../lib/libhpp-fcl.so: undefined symbol: _ZNK6Assimp8IOSystem16CurrentDirectoryB5cxx11Ev

At:
  /home/boxing/my-pin-venv/lib/python3.10/site-packages/cmeel.prefix/lib/python3.10/site-packages/pinocchio/__init__.py(6): <module>
  <frozen importlib._bootstrap>(241): _call_with_frames_removed
  <frozen importlib._bootstrap_external>(883): exec_module
  <frozen importlib._bootstrap>(703): _load_unlocked
  <frozen importlib._bootstrap>(1006): _find_and_load_unlocked
  <frozen importlib._bootstrap>(1027): _find_and_load
  /tmp/carb.nqL1Lv/script_1700530849.py(7): <module>

It seems that this problem relates to libhpp-fcl.so, and the undifined symbol _ZNK6Assimp8IOSystem16CurrentDirectoryB5cxx11Ev relates to Assimp library? Something incompatible with Isaac sim app?

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Import Error while importing Pinocchio #2081

threedee003 Nov 9, 2023

Replies: 2 comments · 9 replies

nim65s Nov 9, 2023 Maintainer

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