Conflict between RDKIT and conda-molgrid

[lh12565]

Hi, I try to install molgrid using conda-molgrid. When I finished installing molgrid, there was an error installing RDKit:

conda install -c conda-forge rdkit

Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: /
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.                           | failed

I try to install rdkit from source, but there is still an error:

make[1]: *** [Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/all] Error 2
[ 61%] Linking CXX static library libRDKitDescriptors_static.a
[ 61%] Built target Descriptors_static
[ 61%] Linking CXX executable graphmolMolOpsTest
/NAS/lh/software/miniconda3/envs/molgrid/bin/../lib/gcc/x86_64-conda-linux-gnu/9.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: warning: libboost_iostreams-mt.so.1.53.0, needed by /usr/local/lib/libmaeparser.so, not found (try using -rpath or -rpath-link)
/NAS/lh/software/miniconda3/envs/molgrid/bin/../lib/gcc/x86_64-conda-linux-gnu/9.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: warning: libboost_regex-mt.so.1.53.0, needed by /usr/local/lib/libmaeparser.so, not found (try using -rpath or -rpath-link)
/NAS/lh/software/miniconda3/envs/molgrid/bin/../lib/gcc/x86_64-conda-linux-gnu/9.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../../lib/libRDKitFileParsers.so.1.2022.09.1pre: undefined reference to `schrodinger::mae::Block::getIndexedBlock(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
/NAS/lh/software/miniconda3/envs/molgrid/bin/../lib/gcc/x86_64-conda-linux-gnu/9.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../../lib/libRDKitDepictor.so.1.2022.09.1pre: undefined reference to `sketcherMinimizer::setTemplateFileDir(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)'
/NAS/lh/software/miniconda3/envs/molgrid/bin/../lib/gcc/x86_64-conda-linux-gnu/9.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../../lib/libRDKitFileParsers.so.1.2022.09.1pre: undefined reference to `schrodinger::mae::Reader::next(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
collect2: error: ld returned 1 exit status
make[2]: *** [Code/GraphMol/graphmolMolOpsTest] Error 1
make[1]: *** [Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/all] Error 2
make: *** [all] Error 2

[binzhougithub]

@lh12565 , did you solve this? I got the same issue. in the end, I was able to use pip to install rdkit. however pip installed another set of libraries like libboostxxx, I am afraid that there is a chance of confliction because generate.py hung at rdkit at around 27th example.

[INHYEOKSONG]

conda-molgrid If I make the yaml file in the folder a mogrid virtual job like this, it works fine.

Name: Molgrid channel:

• Py Torch
• Conda Forge
• default Dependencies:
• gxx<10
• cmake>=3.18
• cudatoolkit=11.3
• cudatoolkit-dev=11.3
• Python=3.7
• Boost = 1.74
• stupid
• Saifi
• Open barbell = 3
• Py Torch
• Pytest
• rdkit=2020.09.5

[mattragoza]

If you have not yet been able to install the dependencies, please try the detailed installation instructions I have just updated in the README.md and let me know how it goes.