Issue with CosolvKit Code on Google Colab

[pablo-arantes]

Hi,

I hope this message finds you well.

I’ve been trying to run the CosolvKit code on Google Colab, but I’m encountering an issue. While the library installation and import went smoothly, I ran into a problem when attempting to build the system. The error seems to be related to the DGL library.

Here is the error message:

IndexError                                Traceback (most recent call last)
<ipython-input-4-51e3a8740d38> in <cell line: 17>()
     15                                    simulation_format="OPENMM")
     16 
---> 17 cosolvent_system.build()
     18 
     19 # # or you can specify epsilon and sigma parameters of the LJ potential

12 frames
/usr/local/lib/python3.10/site-packages/dgl/sparse/__init__.py in load_dgl_sparse()
     35     if len(path) > 1:
     36         raise ImportError("More than one DGL C++ sparse library found")
---> 37     path = path[0]
     38     if not os.path.exists(path):
     39         raise FileNotFoundError(f"Cannot find DGL C++ sparse library at {path}")

IndexError: list index out of range

You can check the notebook using the following link: https://colab.research.google.com/drive/1rI8eXZcXoM3iJHPSFMG9boAKTjojoNF1?usp=sharing

Thank you for your assistance.

Best regards,

Pablo

[nbruciaferri]

Hi Pablo,

thanks for putting effort in creating a Google Colab for CosolvKit, that would be very useful. Unfortunately I don't know how to help you, I suspect that's more of a Google Colab issue and how the dgl and C++ libraries are handled in general.

I don't have experience with Google Colab or at least not enough to help you. Hopefully someone will contribute to this issue, please let me know if you figure out how to make it work.

Thanks,

Niccolo

[rwxayheee]

Hi @pablo-arantes

You might need to install dgl libraries that are suitable for the platform. Here's a link I got from the official website of DGL:

!pip install  dgl -f https://data.dgl.ai/wheels/torch-2.1/cu121/repo.html

You can insert this as a standalone cell after Install Conda Colab. Running this code cell might need another restart of session, to update imported modules.

See my copy of your Colab notebook here:
https://colab.research.google.com/drive/1MpCvG0E1UDJaxlonS7a63XZ8YycfSI1i?usp=sharing

I was able to run the code block that builds CosolventSystem.

Please let us know if this resolves your issue. Additionally, if you'd like to contribute and share your Colab notebook with the community, please feel free to continue the conversation here. We’d love to hear more about your experience and your recipe for Colab setup.

[pablo-arantes]

Hi All,

Thank you so much for your efforts on this. I've tried the suggested solution, and everything works perfectly. I'm using your code to run simulations with different solvents, and it works nicely.

I will prepare a notebook with input options and system visualization, and get back to you before sharing it with the community.

Thank you so much.

Best,
Pablo