pypointmatcher.cpython-38-x86_64-linux-gnu.so: undefined symbol

[venustar2015]

I am trying to use libpointmatcher with python, but when I import the module, it appears the error 'undefined symbol'. Here is the detailed error information:

Python 3.8.8 (default, Apr 13 2021, 19:58:26) 
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pypointmatcher
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: /home/dfcv/anaconda3/lib/python3.8/site-packages/pypointmatcher.cpython-38-x86_64-linux-gnu.so: undefined symbol: _ZN14PointMatcherIOIfE16plyPropTypeValidERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE

Here is the other information:

(base) dfcv@dfcv-ThinkCentre-M720t-N000:~/venus/code/libpointmatcher/examples/python$ lsb_release -r
Release:        16.04
(base) dfcv@dfcv-ThinkCentre-M720t-N000:~/venus/code/libpointmatcher/examples/python$ getconf LONG_BIT
64
(base) dfcv@dfcv-ThinkCentre-M720t-N000:~/venus/code/libpointmatcher/examples/python$ gcc --version
gcc (Ubuntu 5.4.0-6ubuntu1~16.04.12) 5.4.0 20160609
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

(base) dfcv@dfcv-ThinkCentre-M720t-N000:~/venus/code/libpointmatcher/examples/python$ git --version
git version 2.7.4
(base) dfcv@dfcv-ThinkCentre-M720t-N000:~/venus/code/libpointmatcher/examples/python$ cmake --version
cmake version 3.5.1

CMake suite maintained and supported by Kitware (kitware.com/cmake).
(base) dfcv@dfcv-ThinkCentre-M720t-N000:~/venus/code/libpointmatcher/examples/python$ dpkg -s libboost-dev | grep Version
Version: 1.58.0.1ubuntu1
(base) dfcv@dfcv-ThinkCentre-M720t-N000:~/venus/code/libpointmatcher/examples/python$ dpkg -s libeigen3-dev | grep Version
Version: 3.3~beta1-2
(base) dfcv@dfcv-ThinkCentre-M720t-N000:~/venus/code/libpointmatcher/examples/python$ dpkg -s doxygen | grep Version
Version: 1.8.11-1ubuntu0.1

[pomerlef]

@aguenette any thoughts?

[aguenette]

@venustar2015 Which version of pybind11 did you use? I've compiled the bindings with python3.8 and everything is working. It looks like it cannot find the method plyPropTypeValid from IO.cpp. Can you take a screenshot of cmake-gui? If you check the grouped and advanced checkboxes, you should get something like this:

You can expand only the Ungrouped entries and the PYTHON groups. Thanks!

[venustar2015]

@venustar2015 Which version of pybind11 did you use? I've compiled the bindings with python3.8 and everything is working. It looks like it cannot find the method plyPropTypeValid from IO.cpp. Can you take a screenshot of cmake-gui? If you check the grouped and advanced checkboxes, you should get something like this:

You can expand only the Ungrouped entries and the PYTHON groups. Thanks!

Dear Aguenette, it's very glad to hear from you. The version of pybind11 is v2.5.0 as it's described in tutorials, but I don't know how to check it. I get the screenshot for cmake-gui, but cannot find the "pybind11" entries and "PYTHON" grouped as your screenshot. What is the possible cause for it? Here is the screenshot of cmake-gui:

Hope you have a nice day. Thanks!

[aguenette]

@venustar2015 I don't know why these two groups aren't there. The pybind11 version should appear when you configure libpointmatcher's build directory with cmake, i.e. running cmake .. in the build directory. Could you copy and paste here that output after running this command? I'm also curious to see what's in the BUILD group from cmake-gui.

I'm giving you the output I get when I'm running the cmake .. command in the pybind11's build directory :

-- Building tests with Eigen v3.3.4
-- Boost version: 1.65.1
-- Building interpreter tests using Catch v1.10.0
-- pybind11 v2.5.0
-- Configuring done
-- Generating done
-- Build files have been written to: /home/alexandre/git/pybind11/build

and in libpointmatcher's build directory :

-- Boost version: 1.65.1
-- Found the following Boost libraries:
--   thread
--   filesystem
--   system
--   program_options
--   date_time
--   chrono
--   atomic
-- Boost version: 1.65.1
-- Found the following Boost libraries:
--   thread
--   filesystem
--   system
--   program_options
--   date_time
--   chrono
--   atomic
-- libnabo found, version 1.0.7 (include= libs=)
-- OpenMP found, parallel computer enabled
-- using built-in yaml-cpp, version 0.3.0
   -- text-based configuration enabled
-- API Documentation (doxygen): disabled
-- The Python module will be install at this location : /usr/local/lib/python3.8/dist-packages
-- pybind11 v2.5.0
-- Configuring done
-- Generating done
-- Build files have been written to: /home/alexandre/Libraries/libpointmatcher/build-python3.8

And here's a screenshot with the most relevant groups expanded :

[venustar2015]

Dear Aguenette,

Thanks very much for your reply. Here is the info in pybind11/build directory foy cmake ..

(base) dfcv@dfcv-ThinkCentre-M720t-N000:~/venus/code/pybind11/build$ cmake ..
-- Building tests with Eigen v3.2.92
-- Boost version: 1.58.0
-- Catch not detected. Interpreter tests will be skipped. Install Catch headers manually or use `cmake -DDOWNLOAD_CATCH=1` to fetch them automatically.
-- pybind11 v2.5.0
-- Configuring done
-- Generating done
-- Build files have been written to: /home/dfcv/venus/code/pybind11/build

Here's the info in libpointmatcher/build directory for cmake ..

(base) dfcv@dfcv-ThinkCentre-M720t-N000:~/venus/code/libpointmatcher/build$ cmake ..
-- Boost version: 1.58.0
-- Found the following Boost libraries:
--   thread
--   filesystem
--   system
--   program_options
--   date_time
--   chrono
--   atomic
-- Boost version: 1.58.0
-- Found the following Boost libraries:
--   thread
--   filesystem
--   system
--   program_options
--   date_time
--   chrono
--   atomic
-- libnabo found, version 1.0.7 (include= libs=)
-- OpenMP found, parallel computer enabled
-- using built-in yaml-cpp, version 0.3.0
   -- text-based configuration enabled
-- API Documentation (doxygen): disabled
-- The Python module will be install at this location : /home/dfcv/anaconda3/lib/python3.8/site-packages
-- pybind11 v2.5.0
-- Configuring done
-- Generating done
-- Build files have been written to: /home/dfcv/venus/code/libpointmatcher/build

Here is the cmake-gui info. After I check BUILD_PYTHON_MOUDLE and uncheck BUILD_TESTS in BUILD group, and configure again, the PYTHON group and pybind11 info appears, just like below.

However, the error undefined symbol still exists.