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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