IF you want to use some other python install you could try pointing your PYTHONPATH at the directory in your conda environment where the RDKit is installed and make sure that LD_LIBRARY_PATH is pointing to the appropriate lib directory in that conda environment. IF that doesn't work, we likely won’t be able to help though.
It would be a ton easier if you installed whatever other stuff you need in the conda environment or set your PYTHONPATH to point to wherever that stuff is -greg On Wed, 1 Apr 2020 at 18:41, Navid Shervani-Tabar <nshe...@gmail.com> wrote: > Any suggestions on how to get it to work? I tried to get rid of the need > for an environment in RDKit installation using conda-forge on remote > machine but I need access beyond a user. For packages with pip > installation available, *pip install --user* does the job. > > Navid > > On Wed, Apr 1, 2020 at 12:31 PM Greg Landrum <greg.land...@gmail.com> > wrote: > >> That isn’t the python that comes from your conda environment >> >> On Wed, 1 Apr 2020 at 16:58, Navid Shervani-Tabar <nshe...@gmail.com> >> wrote: >> >>> Here are the outputs: >>> >>> (Navid_env) [nshervan@qa-v100-004 ~/Private/Research/Scattering-VAE ]which >>> python3 >>> >>> /afs/crc.nd.edu/x86_64_linux/p/pytorch/1.0.0/build-new/bin/python3 >>> >>> (Navid_env) [nshervan@qa-v100-004 ~/Private/Research/Scattering-VAE ]python3 >>> -c "from rdkit import Chem;print(Chem.__file__)" >>> >>> Traceback (most recent call last): >>> >>> File "<string>", line 1, in <module> >>> >>> ModuleNotFoundError: No module named 'rdkit' >>> >>> (Navid_env) [nshervan@qa-v100-004 ~/Private/Research/Scattering-VAE ] >>> >>> Navid >>> >>> On Wed, Apr 1, 2020 at 10:40 AM Greg Landrum <greg.land...@gmail.com> >>> wrote: >>> >>>> Are you sure that you get the python from your environment when you do >>>> "python3 main.py"? >>>> >>>> Please try these two commands: >>>> >>>> which python3 >>>> python3 -c "from rdkit import Chem;print(Chem.__file__)" >>>> >>>> >>>> >>>> On Tue, Mar 31, 2020 at 11:17 PM Navid Shervani-Tabar < >>>> nshe...@gmail.com> wrote: >>>> >>>>> Hello RDKiters, >>>>> >>>>> I have been using rdkit on my laptop for a while. I was trying to >>>>> install it on my remote repository using conda-forge. It looks like I was >>>>> able to install it but I still get the following error >>>>> >>>>> (Navid_env) [*****@crcfe01 ~/Private/Research/code ] conda install -c >>>>> conda-forge rdkit >>>>> >>>>> Collecting package metadata (current_repodata.json): done >>>>> >>>>> Solving environment: done >>>>> >>>>> >>>>> >>>>> ==> WARNING: A newer version of conda exists. <== >>>>> >>>>> current version: 4.8.2 >>>>> >>>>> latest version: 4.8.3 >>>>> >>>>> >>>>> Please update conda by running >>>>> >>>>> >>>>> $ conda update -n base -c defaults conda >>>>> >>>>> >>>>> >>>>> >>>>> # All requested packages already installed. >>>>> >>>>> >>>>> (Navid_env) [*****@crcfe01 ~/Private/Research/code ] python3 main.py >>>>> >>>>> Traceback (most recent call last): >>>>> >>>>> File "main.py", line 6, in <module> >>>>> >>>>> from VAEtrain import VAEgraph >>>>> >>>>> File "/afs/ >>>>> crc.nd.edu/user/n/*****/Private/Research/Scattering-VAE/VAEtrain.py", >>>>> line 22, in <module> >>>>> >>>>> from utils import tools >>>>> >>>>> File "/afs/ >>>>> crc.nd.edu/user/n/*****/Private/Research/Scattering-VAE/utils.py", >>>>> line 6, in <module> >>>>> >>>>> from rdkit import Chem >>>>> >>>>> ModuleNotFoundError: No module named 'rdkit' >>>>> >>>>> Any idea what might be wrong? (and yes, I have logged in and out >>>>> before running). >>>>> >>>>> Thanks, >>>>> Navid >>>>> _______________________________________________ >>>>> Rdkit-discuss mailing list >>>>> Rdkit-discuss@lists.sourceforge.net >>>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >>>>> >>>>
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