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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