Hi, I am trying to work out how to get the right format for the dependencies when converting my repo ( https://github.com/johnjarmitage/percolation-inversion ) with mybinder. I include the following in the environments.yml: name: percolation channels: - conda-forge - pytorch dependencies: - pyt…

I suspect if you temporarily tie yourself to the old cluster and try https://gke.mybinder.org/v2/gh/johnjarmitage/percolation-inversion/master (note the gke in the domain name, you shouldn’t generally rely on that or hard code it) it’ll work.

I was wrong. This problem has nothing to do with the registry issues. Using my admin powers to look at the log from the container I see: $ kubectl logs -f jupyter-johnjarmitage-2dp-2dation-2dinversion-2dmhd6xpcd /srv/conda/envs/notebook/compiler_compat/ld: cannot find -lpthread /srv/conda/envs/not…

Thanks Tim! I am testing random notebooks on mybinder to see how it works and how the dependencies get dealt with as part of the reproducible journal idea I discussed earlier this week. Therefore, while I don’t need pytorch I thought I would put it in there as it is a typical machine learning depend…

I switched out the pytorch dependency from conda to pip, but it looks like it is still failing. The error message is as before. Is it possible that the notebook dependencies are too demanding? It takes a long time to build, and I had a similar problem with readthedocs (although their machines are sm…

I’ve not looked into it yet but the error message I posted above points more at a discrepancy at the C library level. So not something related to binder/repo2docker but the result of mixing libraries together that aren’t compatible. In general if you want to see a bit more from the build process I’…

Same problem locally in repo2docker with pytorch installed using pip. Could it be a problem related to mixing conda and pip in the environment.yml?

Success! I found the guidelines to making an environment.yml on the repo2docker docs: https://repo2docker.readthedocs.io/en/latest/howto/export_environment.html . I followed them, added my dependencies and the binder image works. (I guess it is not straight forward to automate the manual process of c…

[image] johnjarmitage: I guess it is not straight forward to automate the manual process of creating the precise dependencies for a conda install? There are a few projects which try and guess from analysing Python code what dependencies it has and what the packages for those dependencies coul…

Internal Server Error with notebook with conda dependencies

Binder

betatim June 20, 2019, 8:48pm 2

I think this is nothing to do with you but more to do with the issue discussed here. We recently added a second cluster to mybinder.org and there are still some things that need straightening out :-/.

Topic		Replies	Views
Mybinder (and binderhub) fails for conda environment.yml containing python dependency BinderHub help-wanted	2	896	October 19, 2023
MyBinder stopped working for Repo mybinder.org ops help-wanted	3	1007	September 20, 2023
Module Not Found Error -when running the ipynb notebook- via BINDER session Binder	3	2101	June 11, 2020
Binder getting stuck while installing conda's environment.yml repo help	4	4693	April 8, 2021
Build completes successfully then "Binder Inaccessible" repo help help-wanted	11	1044	January 2, 2023

Internal Server Error with notebook with conda dependencies

Related topics