python interface doesn't work

[cslxiao]

I build python interface and generate libcp.so following the guide, but it cannot be imported in python:

import libcp
malloc(): memory corruption
Aborted (core dumped)

version information:
python: 3.6
boost: 1.65
os: ubuntu 18.04
g++: 6.4

[loicland]

Hi,

can you try to run the troubleshooting section in the README of this repo?

[cslxiao]

I didn't use conda to install boost and eigen. Instead, I use the library in the system path and cmake find them well.

cmake .
-- The C compiler identification is GNU 6.4.0
-- The CXX compiler identification is GNU 6.4.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Boost version: 1.65.1
-- Found the following Boost libraries:
-- graph
-- numpy
-- python
-- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython3.6m.so (found version "3.6.6")
PYTHON LIBRARIES ARE /usr/lib/x86_64-linux-gnu/libpython3.6m.so
-- Configuring done
-- Generating done
-- Build files have been written to: /home/XXX/superpoint_graph/partition/cut-pursuit/src

[XBingQian]

Hello, I have met a same problem.
The cmake and make progress works well with log as follows:
------------ply_c-------------
-- The C compiler identification is GNU 5.4.0
-- The CXX compiler identification is GNU 5.4.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Boost version: 1.67.0
-- Found the following Boost libraries:
-- python
-- numpy
Boost includes ARE /usr/local/include
Boost LIBRARIES ARE /usr/lib
-- Found PythonLibs: /home/xbq/anaconda2/envs/py3/lib/libpython3.6m.so (found version "3.6.6")
PYTHON LIBRARIES ARE /home/xbq/anaconda2/envs/py3/lib/libpython3.6m.so
-- Configuring done
-- Generating done
-- Build files have been written to: /home/xbq/git/superpoint_graph/partition/ply_c
-------------cut-pursuit--------------
-- The C compiler identification is GNU 5.4.0
-- The CXX compiler identification is GNU 5.4.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Boost version: 1.67.0
-- Found the following Boost libraries:
-- graph
-- numpy
-- Found PythonLibs: /home/xbq/anaconda2/envs/py3/lib/libpython3.6m.so (found version "3.6.6")
PYTHON LIBRARIES ARE /home/xbq/anaconda2/envs/py3/lib/libpython3.6m.so
-- Configuring done
-- Generating done
-- Build files have been written to: /home/xbq/git/superpoint_graph/partition/cut-pursuit/src

The libply_c.so and libcp.so files were successfully generated.
But, when I try to run the partition module in superpoint_graph with partition.py, there are errors in"import libcp"(1) and "import libply_c"(2). And the out message are seperately:
(1) ImportError: ./partition/cut-pursuit/src/libcp.so: undefined symbol: _ZTIN5boost6python7objects21py_function_impl_baseE
(2) ImportError: /usr/lib/libboost_python.so.1.66.0: undefined symbol: PyClass_Type
There are anaconda2 and anaconda3 in my PC environment. And I have change it to python3.6 while compile the module.
Could you help to find where the problem is? Thanks.

[loicland]

Hi,

There are many issues on this subject on the superpoint graph repo. Check out thr followings to see if that helps you:
loicland/superpoint_graph#59

loicland/superpoint_graph#56

loicland/superpoint_graph#13

Let me know if you're still stuck after that.

Also im noticing in your build files that you have a mix of anaconda2 and pupython3.6. What value did you give to $CONDAENV?

[cslxiao]

still not work

[loicland]

What value did you give to $CONDAENV?

Are you sure you have libboost_python.so in your LD_LIBRARY_PATH?

[bach-zouk]

Hi Loic,

Could you perhaps post the desired output of test.py file after libcp is built? I was able to compile libcp fine and get this output after running test.py:

L0-CUT PURSUIT WITH L2 FIDELITY
PARAMETERIZATION = FAST
Graph 5 vertices and 14 edges and observation of dimension 1
Iteration 1 - 3 components - Saturation 0.0 % - Quadratic Energy 0.000 % - Timer 0.204649
Iteration 2 - 3 components - Saturation 100.0 % - Quadratic Energy 0.000 % - Timer 0.204701
All components are saturated

[bach-zouk]

My bad: these results I obtain after with python 2.7 which is not suggested anyways.

[zeroAska]

@XBingQian Have you figured out? I ran into exactly the same error as you, libcp.so: undefined symbol: _ZTIN5boost6python7objects21py_function_impl_baseE