Hi Max,
please share the cmake/make outputs with me off-list and I'll try to help.
Cheers,
p.
On 15/04/2020 17:33, Max Pinheiro Jr wrote:
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 <mailto: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
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
<mailto:Rdkit-discuss@lists.sourceforge.net>
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
