Test failure when build with libc++

[oraluben]

Hi, I'm trying to build pyosmium with libc++ on Debian and got an interesting failure.
The build was successful but few tests failed with an unexpected exception thrown:

..........................................EE..............E......E.......................................................
======================================================================
ERROR: test_clear (test_index.TestLocationTable)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/pyosmium/test/test_index.py", line 42, in test_clear
    self.table.get(593)
RuntimeError: id 593 not found

You might notice that the error message is correct but not the error class.
I dug around and found this try-catch is not working well: https://github.com/osmcode/pyosmium/blob/master/lib/osmium.cc#L20-L26

I came up with some small PoC, trying to identify the root cause but have no luck. libc++ seems to have no issue work together with libstdc++ and exception.

Could you please take some time to see if you've got any idea about this? I would be greatful since I'm not very familiar with the code itself.

Build script I use in a debian:buster docker image:

apt-get update

apt-get install -y -qq libboost-dev libexpat1-dev zlib1g-dev libbz2-dev libproj-dev libgeos-dev liblz4-dev cmake

apt-get install -y -qq python3-pip git
pip3 install nose shapely setuptools

git clone https://github.com/osmcode/pyosmium.git

cd pyosmium
git clone --quiet --depth 1 https://github.com/osmcode/libosmium.git contrib/libosmium
git clone --quiet --depth 1 https://github.com/mapbox/protozero.git contrib/protozero
git clone --quiet --depth 1 https://github.com/pybind/pybind11.git contrib/pybind11

apt-get install -y libc++1 libc++-dev
# https://libcxx.llvm.org/docs/UsingLibcxx.html
export CXXFLAGS="-nostdinc++ -I/usr/lib/llvm-7/include/c++/v1"
export LDFLAGS="-nodefaultlibs -L/usr/lib/llvm-7/lib -lc++ -lc++abi -lm -lc -lgcc_s -lgcc"
ln -s /usr/lib/llvm-7/lib/libc++abi.so.1 /usr/lib/llvm-7/lib/libc++abi.so

python3 setup.py build
cd test && python3 run_tests.py

[joto]

I would expect that you have to build python and all python packages used with the same libc++.

[oraluben]

Not exactly, I tried with a library built with libstdc++, pybind11 binding library built with libc++, and the Python come with Debian (also libstdc++).

In this case the error handling works as expected. So I guess there's also some factor related to the package itself. I will upload this demo later.

[oraluben]

In this case the fake_osmium with libstdc++, the binding fake_pyosmium with libc++ and the default python work as expected:

root@7e26f4f8fcde:/# LD_LIBRARY_PATH="/usr/lib/llvm-7/lib" python -c "import fake_pyosmium; fake_pyosmium.foo()"
Traceback (most recent call last):
  File "<string>", line 1, in <module>
KeyError: ''

repro script compatiable with buster Debian

set -e

rm -rf *.o *.so
apt-get update && apt-get install -yqq g++ pybind11-dev python-dev libc++1 libc++-dev

cat >fake_osmium.h <<EOF
#include <stdexcept>
struct not_found : public std::runtime_error {
    explicit not_found(const char* what) :
        std::runtime_error(what) {
    }
};
void foo();
EOF

cat >fake_osmium.cc <<EOF
#include "fake_osmium.h"

void foo() {
    throw not_found{""};
}
EOF

g++ -fPIC -std=c++11 -c fake_osmium.cc -o fake_osmium.o

cat >fake_pyosmium.cc <<EOF
#include "fake_osmium.h"

#include <pybind11/pybind11.h>

namespace py = pybind11;

PYBIND11_MODULE(fake_pyosmium, m) {
    py::register_exception_translator([](std::exception_ptr p) {
        try {
            if (p) std::rethrow_exception(p);
        } catch (const not_found &e) {
            PyErr_SetString(PyExc_KeyError, e.what());
        }
    });

    m.def("foo", &foo);
};
EOF

ln -s /usr/lib/llvm-7/lib/libc++abi.so.1 /usr/lib/llvm-7/lib/libc++abi.so || true
g++ -fPIC -shared -nostdinc++ -I/usr/lib/llvm-7/include/c++/v1 -I/usr/include/pybind11 -I/usr/include/python2.7 fake_osmium.o fake_pyosmium.cc \
  -nodefaultlibs -L/usr/lib/llvm-7/lib -lc++ -lc++abi -lm -lc -lgcc_s -lgcc \
  -o fake_pyosmium.so

LD_LIBRARY_PATH="/usr/lib/llvm-7/lib" python -c "import fake_pyosmium; fake_pyosmium.foo()"

[oraluben]

pybind/pybind11#2847

[lonvia]

This has been resolved in libosmium. The PR mentions that changes to the pyosmium build might be necessary. If that is the case, please open a PR with the proposed changes. Closing here.