Re: [Rdkit-discuss] ImportError: No module named rdkit

[Markus S. <mar...@gm...>]

BTW, python 3.6 is out since last Christmas ;-)   (and made it to
sub-release .2)

On Fri, Sep 15, 2017 at 8:36 AM, Greg Landrum <gre...@gm...>
wrote:

> 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 <lor...@fu...
> > wrote:
>
>> Hi Greg,
>>
>> Greg Landrum <gre...@gm...> writes:
>>
>> > Hi Loris,
>> >
>> > On Thu, Sep 14, 2017 at 2:25 PM, Loris Bennett <
>> lor...@fu...> 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 lor...@fu...
>>
>
>
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