Can not install dependencies in all notebooks.

[noumanistic]

downloading dependencies is giving error.
if one is fixed by any chance another appears.

[pablo-arantes]

Can you please be more specific? Which notebook are you having errors? And are you using the last version available in the Making it Rain site?

[noumanistic]

I am using this notebook. https://colab.research.google.com/github/pablo-arantes/making-it-rain/blob/main/Protein_ligand.ipynb while installing dependencies it gives error about pytraj first. when i install it separate code, it then gives error about openmm. please have a look on it so you will also see there are number of errors. [image: image.png] [image: image.png]

…

On Fri, Dec 15, 2023 at 2:36 AM Pablo Ricardo Arantes < ***@***.***> wrote: Can you please be more specific? Which notebook are you having errors? And are you using the last version available in the Making it Rain site? — Reply to this email directly, view it on GitHub <#93 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A5UVEOYLUZPBE3L7KYMH3SLYJNWMFAVCNFSM6AAAAABAVQCRIGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNJWGY3DQOBXHE> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[noumanistic]

[ysa123-2]

I meet some problem

[zjun028]

Same problem

[andrewsb8]

I'm coming across this as well. It appears to be an issue with conda and the cudatoolkit package:

!mamba install openmm -c conda-forge -y

Looking for: ['openmm']

conda-forge/linux-64                                        Using cache
conda-forge/noarch                                          Using cache
No package can be installed for pin: cudatoolkit 12.2.*

# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

    Traceback (most recent call last):
      File "/usr/local/lib/python3.10/site-packages/conda/exceptions.py", line 1124, in __call__
        return func(*args, **kwargs)
      File "/usr/local/lib/python3.10/site-packages/mamba/mamba.py", line 941, in exception_converter
        raise e
      File "/usr/local/lib/python3.10/site-packages/mamba/mamba.py", line 934, in exception_converter
        exit_code = _wrapped_main(*args, **kwargs)
      File "/usr/local/lib/python3.10/site-packages/mamba/mamba.py", line 892, in _wrapped_main
        result = do_call(parsed_args, p)
      File "/usr/local/lib/python3.10/site-packages/mamba/mamba.py", line 754, in do_call
        exit_code = install(args, parser, "install")
      File "/usr/local/lib/python3.10/site-packages/mamba/mamba.py", line 547, in install
        solver.add_pin(final_spec)
    RuntimeError: No package can be installed for pin: cudatoolkit 12.2.*

`$ /usr/local/bin/mamba install openmm -c conda-forge -y`

  environment variables:
                 CIO_TEST=<not set>
COLAB_DEBUG_ADAPTER_MUX_PATH=/usr/local/bin/dap_multiplexer
COLAB_LANGUAGE_SERVER_PROXY=<set>
               CONDA_ROOT=/usr/local
           CURL_CA_BUNDLE=<not set>
          LD_LIBRARY_PATH=/usr/local/lib:/usr/local/nvidia/lib:/usr/local/nvidia/lib64
               LD_PRELOAD=<not set>
             LIBRARY_PATH=/usr/local/cuda/lib64/stubs
                     PATH=/opt/bin:/usr/local/nvidia/bin:/usr/local/cuda/bin:/usr/local/sbin:/us
                          r/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/tools/node/bin:/tools/googl
                          e-cloud-sdk/bin
               PYTHONPATH=/env/python
           PYTHONWARNINGS=ignore:::pip._internal.cli.base_command
       REQUESTS_CA_BUNDLE=<not set>
            SSL_CERT_FILE=<not set>
               TCLLIBPATH=/usr/share/tcltk/tcllib1.20

     active environment : None
       user config file : /root/.condarc
 populated config files : /usr/local/.condarc
          conda version : 23.1.0
    conda-build version : not installed
         python version : 3.10.10.final.0
       virtual packages : __archspec=1=x86_64
                          __glibc=2.35=0
                          __linux=6.1.58=0
                          __unix=0=0
       base environment : /usr/local  (writable)
      conda av data dir : /usr/local/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
          package cache : /usr/local/pkgs
                          /root/.conda/pkgs
       envs directories : /usr/local/envs
                          /root/.conda/envs
               platform : linux-64
             user-agent : conda/23.1.0 requests/2.28.2 CPython/3.10.10 Linux/6.1.58+ ubuntu/22.04.3 glibc/2.35
                UID:GID : 0:0
             netrc file : None
           offline mode : False


An unexpected error has occurred. Conda has prepared the above report.

The same problem prevents !mamba install -c conda-forge gcc=12.1.0 -y and manual install commands like !mamba install -c conda-forge cudatoolkit=12.1 -y do not change the outcome. The "pin" to cudatoolkit=12.2.* persists.

[pablo-arantes]

Hi All,

I've corrected all the notebooks, and everything should be functioning properly now. Please try again and let me know if you encounter any issues.

Thank you.

Pablo