Hi Greg, Greg Landrum <greg.land...@gmail.com> writes:
> Hi Loris, > > On Thu, Sep 14, 2017 at 2:25 PM, Loris Bennett <loris.benn...@fu-berlin.de> > wrote: > > I am trying to install RDKit on a university cluster running Linux from > source. The build seem to go OK and 'make install' copied the > directories > > lib > rdkit > > to the NFS share where the software should reside. I then do > > export RDBASE=/cm/shared/apps/rdkit/rdkit_2017_03_3 > export PYTHONPATH=$PYTHONPATH:$RDBASE > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$RDBASE/lib > > However when I then run Python (2.6.6) and try > > Just to do some expectation management: python 2.6 is pretty ancient > and there's no guarantee that all of the RDKit code will work with > it. Python 2.7 is the minimum version that we "officially" > support. It's a very good idea to update. OK. I didn't notice that 2.6 was deprecated - maybe this could be explicitly mentioned in the install instructions. I'm running the RedHat clone Scientific Linux 6, so everything in this thread on RH/Python applies. So I can use either Python 2.7 or Python 3.5. I can ask the users what they prefer - although, as you seem know my users here in Berlin, maybe you know too ;-) > import rdkit > > I get > > ImportError: No module named rdkit > > I am not a Python person and my naive expectation was that there should > be a file called > > rdkit.py > > Based on the info provided so far, there should be a directory called > rdkit in the directory: /cm/shared/apps/rdkit/rdkit_2017_03_3 This directory exists. > That directory should contain a number of sub dirs, other files, and a > file called __init__.py (this is the one that tells Python that it can > import the directory as a package). What do you see there? The directory just contains lib rdkit an nothing else, in particular, no __init__.py. I have plenty of __init__.pys in the build directory, so I assume I must have done some thing wrong when running cmake and/or make install. I must admit that I found the installation instructions somewhat unclear on that point. I would find it clearer if things were couched in terms of 'source' and 'destination'. For me, as a make-guy rather than a cmake-guy, it would also be helpful if it were made clearer at which point the destination directory should be specified. I ended up with RDKit being installed under a very long path with included both my intended path and the original build path, so I had to move things around and may have goofed up at that point. > which has to be on my PYTHONPATH. However, since the unpacked sources > together with the build don't seem to contain such a file, either > something is broken or the rdkit module should be found by some other > mechanism. > > Again, based on the info above, I would expect that you want "make > install" to copy the "rdkit" and "lib" directories (as well as a > couple others) to /cm/shared/apps/rdkit/rdkit_2017_03_3. Once we > figure out what actually happened I can maybe help you figure out how > to fix it. This is what I did: module add boost # this just sets the boost stuff up export VERSION=2017_03_3 export RDBASE=/home/BUILD/rdkit/rdkit-rdkit-Release_${VERSION} export LD_LIBRARY_PATH=${RDBASE}:${LD_LIBRARY_PATH} export DESTDIR=/cm/shared/apps/rdkit/${VERSION} and then probably cmake -DCMAKE_INSTALL_PREFIX=/cm/shared/apps/rdkit/${VERSION} so I may have over-egged my install-path-cake. I started all the fiddling with DESTDIR and CMAKE_INSTALL_PREFIX, because my initial attempt resulted in the destination directory being the same as the build directory, which didn't work so well. Thanks for the help - I'll have another go Python 3.5 and try to keep my eye on __init__.py. Cheers, 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