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 🙂