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
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