Dear all, I have exhaustively tried to compile rdkit (latest git version) on a Linux cluster but the compilation process was always failing at the same point with an error message related to the boost library. After searching in the forum, the only way I could surpass the problem and finally get the program compiled was setting the flag "RDK_USE_BOOST_SERIALIZATION" to OFF. However, when I do a simple test trying to import the Chem module I get the following error:
-------------------------------------------------------------------------------------------------------- from rdkit import Chem Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/home/mpinheiro/codes/rdkit-2020.09/rdkit/Chem/__init__.py", line 20, in <module> from rdkit.Chem import rdchem SystemError: initialization of rdchem raised unreported exception -------------------------------------------------------------------------------------------------------- I am using gcc-8.1, cmake-3.11.2 and the version 1.67 of boost library to build RDKit. The compilation instructions I have used are the following: cmake -DPy_ENABLE_SHARED=1 \ -DRDK_INSTALL_INTREE=ON \ -DRDK_BUILD_CPP_TESTS=ON \ -DRDK_INSTALL_STATIC_LIBS=ON \ -DRDK_BUILD_AVALON_SUPPORT=ON \ -DRDK_BUILD_CAIRO_SUPPORT=ON \ -DRDK_BUILD_INCHI_SUPPORT=ON \ -DRDK_BUILD_PYTHON_WRAPPERS=ON \ -DRDK_BUILD_SWIG_CSHARP_WRAPPER=ON \ -DPYTHON_EXECUTABLE=/home/mpinheiro/.pyenv/versions/3.8.2/bin/python \ -DPYTHON_LIBRARY=/home/mpinheiro/.pyenv/versions/3.8.2/lib/libpython3.8.a \ -DPYTHON_INCLUDE_DIR=/home/mpinheiro/.pyenv/versions/3.8.2/include/python3.8 \ -DPYTHON_NUMPY_INCLUDE_PATH="$(python -c 'import numpy ; print(numpy.get_include())')" \ -DBOOST_ROOT=/home/mpinheiro/codes/boost-1.67/ \ -DBOOST_INCLUDEDIR=/home/mpinheiro/codes/boost-1.67/include/boost \ -DBOOST_LIBRARYDIR=/home/mpinheiro/codes/boost-1.67/lib .. make -j 4 > make.log make install I have also checked the links created in the rdBase.so file as shown below and everything seems to be fine: linux-vdso.so.1 => (0x00002aaaaaaab000) libRDKitRDBoost.so.1 => /home/mpinheiro/codes/rdkit-2020.09/lib/libRDKitRDBoost.so.1 (0x00002aaaaadb1000) libboost_python38.so.1.67.0 => /home/mpinheiro/codes/boost-1.67/lib/libboost_python38.so.1.67.0 (0x00002aaaaafb5000) libRDKitRDGeneral.so.1 => /home/mpinheiro/codes/rdkit-2020.09/lib/libRDKitRDGeneral.so.1 (0x00002aaaab1fb000) libpthread.so.0 => /usr/lib64/libpthread.so.0 (0x00002aaaab423000) libstdc++.so.6 => /trinity/shared/apps/custom/x86_64/gcc-8.1.0/lib64/libstdc++.so.6 (0x00002aaaab640000) libm.so.6 => /usr/lib64/libm.so.6 (0x00002aaaab9c4000) libgcc_s.so.1 => /trinity/shared/apps/custom/x86_64/gcc-8.1.0/lib64/libgcc_s.so.1 (0x00002aaaabcc6000) libc.so.6 => /usr/lib64/libc.so.6 (0x00002aaaabedf000) librt.so.1 => /usr/lib64/librt.so.1 (0x00002aaaac2a2000) libdl.so.2 => /usr/lib64/libdl.so.2 (0x00002aaaac4aa000) libutil.so.1 => /usr/lib64/libutil.so.1 (0x00002aaaac6af000) /lib64/ld-linux-x86-64.so.2 (0x0000555555554000) As I said, I have tried many different tricks and suggestions that I was able to find in the forum but none of them effectively solved my problem to get the code working. So I would like to ask you if someone has faced a similar problem and may already have some tips on how to fix it. I will really appreciate any help you can provide on this issue. Thanks! Max Pinheiro Jr
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