Rdkit: DLL load failed when Python interpreter is not started from the command line

[michaelosthege]

Hi,

I have a half-working installation. To be more precise:

• I can import rdkit iff the Python interpreter was started from the command line.
• import rdkit fails with an ImportError if I do it from either the interactive window or a debugging session (Visual Studio 2017 RC)

On the windows command line, in the activated venv35 environment:

(venv35) C:\Users\me\Source>python
Python 3.5.2 |Continuum Analytics, Inc.| (default, Jul  5 2016, 11:41:13) [MSC v.1900 64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> from rdkit import Chem
>>> from rdkit.rdBase import rdkitVersion
>>> rdkitVersion
'2016.09.2'

The same environment in the VS interactive window:

>>> from rdkit import Chem
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "C:\Users\me\Miniconda3\envs\venv35\lib\site-packages\rdkit\__init__.py", line 2, in <module>
    from .rdBase import rdkitVersion as __version__
ImportError: DLL load failed: The specified module could not be found.

My hypothesis is that activating the environment from the command line sets environment variables that are not set otherwise. (PYTHONPATH, RDBASE ???)
I tried to track them down, but failed.

I would like to fix this so I can debug my application.

Maybe the appropiate variables can be set just prior to ´import rdkit`?

[greglandrum]

That error is almost certainly due to PATH not being set properly in the second case.
Please compare the two environments and check what is different about the PATH.

[michaelosthege]

Yes, that was it. I am now appending the missing PATH entries before import (and it works)

os.environ["PATH"] += r";C:\Users\me\Miniconda3\envs\venv35"
os.environ["PATH"] += r";C:\Users\me\Miniconda3\envs\venv35\Library\mingw-w64\bin"
os.environ["PATH"] += r";C:\Users\me\Miniconda3\envs\venv35\Library\usr\bin"
os.environ["PATH"] += r";C:\Users\me\Miniconda3\envs\venv35\Library\bin"
os.environ["PATH"] += r";C:\Users\me\Miniconda3\envs\venv35\Scripts"

🎉

[greglandrum]

glad that worked.

[diallobakary4]

I'm experiencing a very similar problem

I have installed conda on windows 10. Then I installed rdkit and create an environment
conda create -c rdkit -n my-rdkit-env rdkit

Now when I active the environment (activate my-rdkit-env), then run python and try to import rdkit.
I ran into the same error as above:

  from .rdBase import rdkitVersion as __version__
ImportError: DLL load failed: The specified module could not be found.

I have tried solution proposed here by adding the paths without success.

os.environ["PATH"] += r";C:\Users\Bakary\AppData\Local\conda\conda\envs\my-rdkit-env\DLLs"
os.environ["PATH"] += r";C:\Users\Bakary\AppData\Local\conda\conda\envs\my-rdkit-env\includ"
os.environ["PATH"] += r";C:\Users\Bakary\AppData\Local\conda\conda\envs\my-rdkit-env\Lib"
os.environ["PATH"] += r";C:\Users\Bakary\AppData\Local\conda\conda\envs\my-rdkit-env\Library"
os.environ["PATH"] += r";C:\Users\Bakary\AppData\Local\conda\conda\envs\my-rdkit-env\libs"
os.environ["PATH"] += r";C:\Users\Bakary\AppData\Local\conda\conda\envs\my-rdkit-env\Scripts"
os.environ["PATH"] += r";C:\Users\Bakary\AppData\Local\conda\conda\envs\my-rdkit-env\Library\usr\bin"
os.environ["PATH"] += r";C:\Users\Bakary\AppData\Local\conda\conda\envs\my-rdkit-env\Library\bin"
os.environ["PATH"] += r";C:\Users\Bakary\AppData\Local\conda\conda\envs\my-rdkit-env\Library\include"
os.environ["PATH"] += r";C:\Users\Bakary\AppData\Local\conda\conda\envs\my-rdkit-env\Library\lib"
os.environ["PATH"] += r";C:\Users\Bakary\AppData\Local\conda\conda\envs\my-rdkit-env\Library\share"

I do not know if I'm missing a path entry.
This is the content of the directory C:\Users\Bakary\AppData\Local\conda\conda\envs\my-rdkit-env\ :
conda-meta/ DLLs/ include/ Lib/ Library/ libs/ Scripts/ tcl/ Tools/

Is that mean that I have to add all the paths again to use Rdkit?

It would really nice if someone can help me out.
Thanks a lot!

[greglandrum]

@diallobakary4 Which python version are you using and which version of conda?

[diallobakary4]

I'm using conda 4.4.10 and pyhon 3.5.
But I finally managed to resolve the problem by reinstalling everything. I have the related post on stackoverflow here.
Thank you for your help