Hi Paolo,
Thank you for your quite fast answer! Yes, I compiled Boost 1.67 using the
same gcc version, 8.1. I have seen this GLIBCXX possible solution that you
have commented before, and I also tried that but didn't work anyway, I got
the same problem with the Boost library and the compilation can't finish. I
am wondering if may exist any other solution. I can also provide some other
specific information if this would help to map the problem and find a
solution.
Thank you again!
Max Pinheiro Jr
Em qua., 15 de abr. de 2020 às 18:25, Paolo Tosco <
paolo.tosco.m...@gmail.com> escreveu:
> Hi Max,
>
> you mention you are using gcc-8.1 and Boost 1.67. Did you compile Boost
> with the same compiler or was it compiled with an earlier version of
> gcc/g++?
>
> If Boost was compiled with an earlier version of gcc/g++, you will need to
> add to /home/mpinheiro/codes/rdkit-2020.09/CMakeLists.txt the following
> line:
>
> add_definitions("-D_GLIBCXX_USE_CXX11_ABI=0")
>
> or the linker will fail during the compilation; see
> https://github.com/rdkit/rdkit/issues/2013#issuecomment-553563418.
>
> HTH, cheers
> p.
> On 15/04/2020 17:15, Max Pinheiro Jr wrote:
>
> 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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