Sorry I missed that you were on windows. It looks like you can probably carefully construct an environment manually using the '--no-deps' argument to "conda install"
I created and activated a python 3.7 environment on windows, installed pandas and numpy from pip, and then did: conda install --no-deps libboost py-boost conda install --no-deps -c rdkit rdkit That got me to the point that I can at least import the rdkit and rdkit.Chem, but there are almost certainly some missing dependencies that you'll have to install (either from conda if possible or from pip if not). Note that once you've gone through the dance of making this work, you should be able to can easily re-create the environment http://rdkit.blogspot.com/2019/10/sharing-conda-environments.html -greg On Tue, Nov 12, 2019 at 10:43 AM Thomas Strunz <beginn...@hotmail.de> wrote: > Hi Greg, > > thanks for your quick reply. > > The main problem is windows. This doesn't work on windows (one needs to > add -c anaconda to your command so that nomkl is found) but then this is > the result: > > > eg. it still wants to install mkl together with nomkl. > > best regards, > > Thomas > > > > ------------------------------ > *Von:* Greg Landrum <greg.land...@gmail.com> > *Gesendet:* Dienstag, 12. November 2019 10:13 > *An:* Thomas Strunz <beginn...@hotmail.de> > *Cc:* rdkit-discuss@lists.sourceforge.net < > rdkit-discuss@lists.sourceforge.net> > *Betreff:* Re: [Rdkit-discuss] Anaconda installation without hard > dependency on Intel MKl (windows) > > Hi Thomas, > > I'm not sure how to configure conda so that a pip-installed version of > numpy and/or pandas is used, but you can use conda versions without MKL by > installing the nomkl package. > > This conda command creates a functioning environment that does not have > the MKL installed: > conda create -n no_mkl python=3.7 nomkl numpy pandas scikit-learn > rdkit::rdkit > > (no_mkl) glandrum@otter:~$ python -c 'import > rdkit;print(rdkit.__version__)' > 2019.09.1 > > Does that help? > -greg > > > On Tue, Nov 12, 2019 at 9:53 AM Thomas Strunz <beginn...@hotmail.de> > wrote: > > Dear all, > > would it be possible to make RDKit package not depend on mkl (probably via > numpy, pandas) and that it accepts pre-installed numpy and pandas for > example from pip as sufficient? > > The background to this is simple. Intel MKL cripples performance on any > AMD bases processor (4-5 times slower, SSE vs AVX2). Since these AMD CPUs > are now actually competitive again, this poses an issue. On Linux it's > simple to just link to openblas and it works as far as I can tell just > fine. > > On Windows the issue is that some tools for example scipy and pandas are > only available as openblas builds via pypi (pip). I'm not sure where the > issue is but when I then want to install rdkit into such an environment it > doesn't "accept" the preinstalled numpy and pandas from pip and wants to > install the conda version based on mkl again maybe due to the package > dependencies. > > Can this be changed so that when installing rdkit it accepts numpy and > pandas install from pypi? > > thanks for any help. > > Best regards, > > Thomas > > > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > >
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