C++ ABI Incompatibilities with conda hdf5

[coreyjadams]

If you install via conda, you will likely get a version of hdf5 that is fairly new. Versions 1.10.4 for example are compiled with gcc 7, and use the latest std::string implementations.

https://gcc.gnu.org/onlinedocs/gcc-5.2.0/libstdc++/manual/manual/using_dual_abi.html

If you get errors when you import larcv indicating that it is missing a function for insertMember, and you have used conda to install hdf5, likely this is the problem. The best solution is to rebuild larcv with a newer compiler. If you have access to gcc5 or higher, you can rebuild from source:

cd /path/to/larcv3/
rm -rf _skbuild
CXX=$(which g++-5) CC=$(which gcc-5) python setup.py install -j 12 [--user]

Obviously, replace g++-5/gcc-5 with a different version if that is what you want to use.

[coreyjadams]

The branch hdf5_fix with PR #16 will fix most of the issues with this incompatibility. The only remaining challenge is that the H5::CompType::insertMember function has only a H5std_string version, no char * version. H5std_string is typecast to std::string and therefore the ABI compatibility is inescapable. If you find linking errors relating to std::string and __cx11 std::string, this is almost certainly the cause.