sokrypton / sokrypton/ColabFold
Install fails with notebook relax_amber.ipynb
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Description
On the heels of the recently resolved issue #437––an early fail during the install of dependencies, traced to incompatibility with Amber version used––I've noticed that a ~similar failure occurs during the 'install amber' phase of the (quite useful!) relax_amber.ipynb Colab notebook, after some ~15 min or so of spinning its wheels. Makes sense that the observed Amber issues would also affect this notebook! Anyway, here's the beginning of the very long error msg, followed by the end bit. Thanks again in advance for checking this out!
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Looking in indexes: https://pypi.org/simple, https://us-python.pkg.dev/colab-wheels/public/simple/
Collecting py3dmol
Downloading py3Dmol-2.0.1.post1-py2.py3-none-any.whl (12 kB)
Installing collected packages: py3dmol
Successfully installed py3dmol-2.0.1.post1
PREFIX=/opt/conda
Unpacking payload ...
Installing base environment...
Downloading and Extracting Packages
Downloading and Extracting Packages
Preparing transaction: done
Executing transaction: done
installation finished.
WARNING:
You currently have a PYTHONPATH environment variable set. This may cause
unexpected behavior when running the Python interpreter in Miniconda3.
For best results, please verify that your PYTHONPATH only points to
directories of packages that are compatible with the Python interpreter
in Miniconda3: /opt/conda
env: PATH=/opt/conda/bin:/opt/bin:/usr/local/nvidia/bin:/usr/local/cuda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/tools/node/bin:/tools/google-cloud-sdk/bin
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
Package Plan
environment location: /opt/conda
added / updated specs:
- conda==4.13.0
The following packages will be downloaded:
package | build
---------------------------|-----------------
conda-4.13.0 | py310h06a4308_0 905 KB
ruamel_yaml-0.15.100 | py310h7f8727e_0 490 KB
yaml-0.2.5 | h7b6447c_0 75 KB
------------------------------------------------------------
Total: 1.4 MB
The following NEW packages will be INSTALLED:
ruamel_yaml pkgs/main/linux-64::ruamel_yaml-0.15.100-py310h7f8727e_0
yaml pkgs/main/linux-64::yaml-0.2.5-h7b6447c_0
The following packages will be DOWNGRADED:
conda 23.3.1-py310h06a4308_0 --> 4.13.0-py310h06a4308_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Solving environment: ...working...
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
failed
UnsatisfiableError: The following specifications were found to be incompatible with a past
explicit spec that is not an explicit spec in this operation (pip):
- openmm=7.5.1 -> numpy -> python[version='2.7.|3.5.|3.6.|>=2.7,<2.8.0a0|>=3.10,<3.11.0a0|>=3.11,<3.12.0a0|>=3.5,<3.6.0a0|3.4.|3.7.|3.9.|3.8.*']
- openmm=7.5.1 -> python[version='>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.9,<3.10.0a0|>=3.8,<3.9.0a0']
- pdbfixer -> numpy -> python[version='2.7.|3.5.|3.6.|>=2.7,<2.8.0a0|>=3.10,<3.11.0a0|>=3.11,<3.12.0a0|>=3.8,<3.9.0a0|>=3.9,<3.10.0a0|>=3.7,<3.8.0a0|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0|3.4.|>=3.7|>=3.8']
- pdbfixer -> python[version='>=3.6']
- pdbfixer -> setuptools
- python=3.10 -> pip -> setuptools
- python=3.10 -> pip -> wheel
...
And then the end of the error msg:
CalledProcessError Traceback (most recent call last)
in <cell line: 11>()
24 PATH=get_ipython().run_line_magic('env', 'PATH')
25 get_ipython().run_line_magic('env', 'PATH=/opt/conda/bin:{PATH}')
---> 26 get_ipython().run_line_magic('shell', 'conda install -qy conda==4.13.0 && conda install -qy -c conda-forge python={python_version} openmm=7.5.1 pdbfixer')
27 pbar.update(80)
28
2 frames
/usr/local/lib/python3.10/dist-packages/google/colab/_system_commands.py in check_returncode(self)
135 def check_returncode(self):
136 if self.returncode:
--> 137 raise subprocess.CalledProcessError(
138 returncode=self.returncode, cmd=self.args, output=self.output
139 )
CalledProcessError: Command 'conda install -qy conda==4.13.0 && conda install -qy -c conda-forge python=3.10 openmm=7.5.1 pdbfixer' returned non-zero exit status 1.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with relax_amber.ipynb and reproduce the failure during its install amber phase in Colab. Inspect the conda command installing Python 3.10, OpenMM 7.5.1, and pdbfixer; done means the dependency installation completes and the notebook proceeds past that phase.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- anaconda, jupyter-notebook, python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100