boost-python minimalistic example throws malloc error on macOS

[carsten-forty2]

Issue:
This issue is a sequel to #81
I experience now a weird malloc problem for a minimalistic boost-python example using std::throw in conda environment on macosx.

The given example (see below) was tested on linux, windows and macos, and only the mac version for macos gives:

python(15723,0x109c09dc0) malloc: *** error for object 0x7f95c15011f8: pointer being freed was not allocated
python(15723,0x109c09dc0) malloc: *** set a breakpoint in malloc_error_break to debug

It would be great if you also know a solution or give me some hints to debug this problem.


Environment (conda list):

# Name                    Version                   Build  Channel
boost                     1.70.0           py36hbf1eeb5_1    conda-forge
boost-cpp                 1.70.0               h75728bb_2    conda-forge
bzip2                     1.0.8                h0b31af3_2    conda-forge
ca-certificates           2019.11.28           hecc5488_0    conda-forge
certifi                   2019.11.28               py36_0    conda-forge
icu                       64.2                 h6de7cb9_1    conda-forge
libblas                   3.8.0               14_openblas    conda-forge
libcblas                  3.8.0               14_openblas    conda-forge
libcxx                    9.0.1                         0    conda-forge
libcxxabi                 9.0.1                         0    conda-forge
libffi                    3.2.1             h6de7cb9_1006    conda-forge
libgfortran               4.0.0                         2    conda-forge
liblapack                 3.8.0               14_openblas    conda-forge
libopenblas               0.3.7                h3d69b6c_6    conda-forge
llvm-openmp               9.0.1                h40edb58_0    conda-forge
ncurses                   6.1               h0a44026_1002    conda-forge
numpy                     1.17.3           py36hde6bac1_0    conda-forge
openssl                   1.1.1d               h0b31af3_0    conda-forge
pip                       19.3.1                   py36_0    conda-forge
python                    3.6.7             h4285619_1006    conda-forge
readline                  8.0                  hcfe32e1_0    conda-forge
setuptools                44.0.0                   py36_0    conda-forge
sqlite                    3.30.1               h93121df_0    conda-forge
tk                        8.6.10               hbbe82c9_0    conda-forge
wheel                     0.33.6                   py36_0    conda-forge
xz                        5.2.4             h1de35cc_1001    conda-forge
zlib                      1.2.11            h0b31af3_1006    conda-forge

Details about conda and system ( conda info ):

active environment : base
    active env location : /Users/florian/opt/anaconda3
            shell level : 1
       user config file : /Users/florian/.condarc
 populated config files : /Users/florian/.condarc
          conda version : 4.8.0
    conda-build version : 3.18.11
         python version : 3.6.9.final.0
       virtual packages : __osx=10.15.1
       base environment : /Users/florian/opt/anaconda3  (writable)
           channel URLs : https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /Users/florian/opt/anaconda3/pkgs
                          /Users/florian/.conda/pkgs
       envs directories : /Users/florian/opt/anaconda3/envs
                          /Users/florian/.conda/envs
               platform : osx-64
             user-agent : conda/4.8.0 requests/2.22.0 CPython/3.6.9 Darwin/19.0.0 OSX/10.15.1
                UID:GID : 501:20
             netrc file : None
           offline mode : False

Steps to reproduce:

The minimalistic cpp example (save as bpt.cpp):

#include "boost/python.hpp"
#include <iostream>

void t(){
   std::cout << "test throw std::out_of_range" << std::endl;
   throw std::out_of_range ("std::out_of_range");
}

namespace bp = boost::python;
BOOST_PYTHON_MODULE(_bpt_){
    bp::def("t", t, "");
}

The python test file: (save as bpt.py )

import _bpt_

print(dir(_bpt_))

try:
    _bpt_.t()
except Exception as e:
    print("catched:", e) # Exception will not be catched but throws the malloc problem

A Makefile to build the bindings (save as Makefile ) and you probably need to correct the ENV variable

TARGET=_bpt_

ENV=/Users/florian/opt/anaconda3/envs/boost

PYINC=-I $(ENV)/include/python3.6m/
BPLIB=$(ENV)/lib/libboost_python36.dylib
BPINC=-I $(ENV)/include

CXX=clang++ 
AR=clang++ -bundle -undefined dynamic_lookup

default:

        $(CXX) -fPIC -c bpt.cpp $(PYINC) $(BPINC)
        $(AR) -o $(TARGET).so *.o $(BPLIB)

test:
        python bpt.py

clean:
        rm -f *.o *.so *~

Finally create the environment and test the problem.

conda create -c conda-forge -n boost boost python=3.6
conda activate boost
make
make test

The method t() should throw the exception but the uncatchable malloc problems occurs instead.

Best regards and thank you,
Carsten

[jschueller]

Does not seem related to conda-forge, ask upstream

[isuruf]

Can you remove the libcxxabi package?

[carsten-forty2]

how should I remove the libcxxabi package?

[isuruf]

conda remove libcxxabi

[carsten-forty2]

RemoveError: This operation will remove conda without replacing it with
another version of conda.

[isuruf]

conda remove libcxxabi -n boost

[carsten-forty2]

clang++  -fPIC -c bpt.cpp -I /Users/florian/opt/anaconda3/envs/boost/include/python3.6m/ -I /Users/florian/opt/anaconda3/envs/boost/include
bpt.cpp:1:10: fatal error: 'boost/python.hpp' file not found
#include "boost/python.hpp"
         ^~~~~~~~~~~~~~~~~~

no clue how this happen now

[carsten-forty2]

okay fresh environment and the problem seems to be gone .. I need to check my tool chains now.

Thanks a lot.

[jakirkham]

People often install the compilers package to do development in a Conda environment. Maybe this will work nicer for you 🙂