Hi Max,
Not sure if it will help, but on Debian and Ubuntu you need the
following
system packages to be installed in order to compile rdkit:
curl
wget
libboost-all-dev
cmake
git
g++
libeigen3-dev
python3
libpython3-all-dev
python3-numpy
python3-pip
python3-pil
python3-six
python3-pandas
What Linux distro are you using?
Doesn't your distribution provides python3 ready packages for rdkit?
Ideally, this is what you would want, especially if you install rdkit on
all nodes of a computing cluster.
Regards,
F.
On 16/04/2020 01:33, 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> 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
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
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
