I'll provide a more detailed answer in a bit, but since you aren't using
the system python anyway, is there any chance that you could switch to
anaconda python on your machines? Anaconda is a great python distribution
for scientific applications and it makes many things (including system
administration) a ton easier.

-greg


On Fri, Sep 15, 2017 at 8:19 AM, Loris Bennett <loris.benn...@fu-berlin.de>
wrote:

> 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 Universit├Ąt Berlin         Email loris.benn...@fu-berlin.de
>
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