Dear all:
So I did a little more testing and I found the solution.
I used exactly the same version of gcc and g++ compilers as Greg did.
Also, I needed to remove the
'add_definitions("-D_GLIBCXX_USE_CXX11_ABI=0")' line in the CMakeLists.txt
file.
Now the compilation and the compiled test program work like charm 😄.
All the best,
MarkusOn Wed, Oct 13, 2021 at 2:28 PM Markus Metz <metm...@gmail.com> wrote: > Dear all: > I would like to repeat Greg's example here: > > https://greglandrum.github.io/rdkit-blog/tutorial/technical/2021/07/24/setting-up-a-cxx-dev-env.html > > Working on Centos 7.6 and the 2021.03.5 rdkit release > I followed all the steps and used the exact same input files. > > I have set the env variable as: > export RDBASE=/.../anaconda3/envs/rdkit_dev > export PYTHONPATH=$RDBASE > > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH: > .../anaconda3/envs/rdkit_dev/include > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:../anaconda3/envs/rdkit_dev/lib > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH: .../anaconda3/lib > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH: .../anaconda3/include > > I then set the g++ and gcc compilers with the CXX and CC env variables: > export CXX=/usr/local/bin/g++ > export CC=/usr/local/bin/gcc > > The cmake step seems to work. Here is the output: > -- The C compiler identification is GNU 8.3.0 > -- The CXX compiler identification is GNU 8.3.0 > -- Detecting C compiler ABI info > -- Detecting C compiler ABI info - done > -- Check for working C compiler: /usr/local/bin/gcc - skipped > -- Detecting C compile features > -- Detecting C compile features - done > -- Detecting CXX compiler ABI info > -- Detecting CXX compiler ABI info - done > -- Check for working CXX compiler: /usr/local/bin/g++ - skipped > -- Detecting CXX compile features > -- Detecting CXX compile features - done > -- Looking for pthread.h > -- Looking for pthread.h - found > -- Performing Test CMAKE_HAVE_LIBC_PTHREAD > -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed > -- Looking for pthread_create in pthreads > -- Looking for pthread_create in pthreads - not found > -- Looking for pthread_create in pthread > -- Looking for pthread_create in pthread - found > -- Found Threads: TRUE > -- Found Boost: ... > anaconda3/envs/rdkit_dev/lib/cmake/Boost-1.74.0/BoostConfig.cmake (found > suitable version "1.74.0", minimum required is "1.74.0") > -- Found Boost: ... > /anaconda3/envs/rdkit_dev/lib/cmake/Boost-1.74.0/BoostConfig.cmake (found > version "1.74.0") found components: timer system > -- Configuring done > -- Generating done > -- Build files have been written to: ... /c++/rdkit/example/build > > But the next step, the linking process, throws me errors: > > [ 50%] Building CXX object CMakeFiles/tautomer_hash.dir/tautomer_hash.cpp.o > [100%] Linking CXX executable tautomer_hash > CMakeFiles/tautomer_hash.dir/tautomer_hash.cpp.o: In function > `readmols(std::string, unsigned int, > std::vector<boost::shared_ptr<RDKit::RWMol>, > std::allocator<boost::shared_ptr<RDKit::RWMol> > >&)': > tautomer_hash.cpp:(.text+0x7f): undefined reference to > `RDKit::SmilesMolSupplier::SmilesMolSupplier(std::string const&, > std::string const&, int, int, bool, bool)' > CMakeFiles/tautomer_hash.dir/tautomer_hash.cpp.o: In function > `generatehashes(std::vector<boost::shared_ptr<RDKit::RWMol>, > std::allocator<boost::shared_ptr<RDKit::RWMol> > > const&)': > tautomer_hash.cpp:(.text+0x29f): undefined reference to > `RDKit::MolHash::MolHash(RDKit::RWMol*, RDKit::MolHash::HashFunction)' > /home/mmetz/anaconda3/envs/rdkit_dev/lib/libRDKitGraphMol.so.1.2021.03.5: > undefined reference to `std::__cxx11::basic_istringstream<char, > std::char_traits<char>, std::allocator<char> > >::basic_istringstream()@GLIBCXX_3.4.26' > /home/mmetz/anaconda3/envs/rdkit_dev/lib/libRDKitFileParsers.so.1.2021.03.5: > undefined reference to `std::__cxx11::basic_ostringstream<char, > std::char_traits<char>, std::allocator<char> > >::basic_ostringstream()@GLIBCXX_3.4.26' > /home/mmetz/anaconda3/envs/rdkit_dev/lib/libRDKitFileParsers.so.1.2021.03.5: > undefined reference to `std::__cxx11::basic_stringstream<char, > std::char_traits<char>, std::allocator<char> > >::basic_stringstream()@GLIBCXX_3.4.26' > collect2: error: ld returned 1 exit status > make[3]: *** [tautomer_hash] Error 1 > make[2]: *** [CMakeFiles/tautomer_hash.dir/all] Error 2 > make[1]: *** [CMakeFiles/tautomer_hash.dir/rule] Error 2 > make: *** [tautomer_hash] Error 2 > > I checked around on the web and could find some info on 'std::__cxx11:' > which seems to indicate ... 'to link together object files that were > compiled with different values for the _GLIBCXX_USE_CXX11_ABI macro' > > And I used Paolo's suggestion > 'add_definitions("-D_GLIBCXX_USE_CXX11_ABI=0")' in the CMakefile.txt. No > change. > > Does anybody know what is going on? > Thank you very much in advance. > Best, > Markus > >
_______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
