Hi Greg, Greg Landrum <greg.land...@gmail.com> writes:
> One thing that may help is this (somewhat older, but I believe still > accurate) post from Riccardo: > https://sourceforge.net/p/rdkit/mailman/message/30074971/ > > It's been a while since I looked at this (since I mainly use conda these > days), but I just did a quick experiment with: > > mkdir build > cd build > cmake -DCMAKE_INSTALL_PREFIX=/opt/rdkit_test -DRDK_INSTALL_INTREE=OFF .. > > followed by > > make install > > and that seems to have worked. > > This type of install behaves somewhat differently from what the > documentation describes. It arranges the files in the PREFIX directory > like "normal" software is arranged. So as a user I need to set my > PYTHONPATH like this: > > export PYTHONPATH=/opt/rdkit_test/lib/python3.5/site-packages > and modify LD_LIBRARY_PATH to include: /opt/rdkit_test/lib > RDBASE is: > export RDBASE=/opt/rdkit_test/share/RDKit > > This is not documented in any useful way, which is something that we > ought to change. OK, I think I have got things mostly working. The -DRDK_INSTALL_INTREE=OFF seems to have been the main thing I was missing. Additionally I had to add some environment variables by hand that cmake didn't pickup on, presumably because due to my having multiple versions of Python installed. This is what I did: export VERSION=2017_03_3 export RDBASE=/home/BUILD/rdkit/rdkit-Release_${VERSION} export LD_LIBRARY_PATH=${RDBASE}:${LD_LIBRARY_PATH} source /cm/shared/apps/python27/enable export PYTHON_ROOT=/opt/rh/python27/root export CMAKE_INSTALL_PREFIX=/cm/shared/apps/rdkit/${VERSION} export PYTHON_INCLUDE_DIR=${PYTHON_ROOT}/usr/include/python2.7 export PYTHON_LIBRARY=${PYTHON_ROOT}/usr/lib64/libpython2.7.so export PYTHON_NUMPY_INCLUDE_PATH=${PYTHON_ROOT}/usr/lib64/python2.7/site-packages/numpy/core/include cmake -DCMAKE_INSTALL_PREFIX=${CMAKE_INSTALL_PREFIX} \ -DPYTHON_INCLUDE_DIR=${PYTHON_INCLUDE_DIR} \ -DPYTHON_LIBRARY=${PYTHON_LIBRARY} \ -DPYTHON_NUMPY_INCLUDE_PATH=${PYTHON_NUMPY_INCLUDE_PATH} \ -DRDK_INSTALL_INTREE=OFF \ .. make make install When I did make test some of the tests failed: 61% tests passed, 46 tests failed out of 117 but most of the failures seemed to have been caused by ImportError: No module named rdkit However, if I set up the user environment (we use modules: http://modules.sourceforge.net/), I can import 'rdkit' without any problem, so there must just be something I need to tweak before running the tests. Thus, apart from the outstanding 46 tests, I think I'm done. Thanks for the help, Loris -- Dr. Loris Bennett (Mr.) ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
