google-deepmind / google-deepmind/alphafold

docker.errors.DockerException: Error while fetching server API version: HTTPConnection.request() got an unexpected keyword argument 'chunked'

Open
#867 26 comments 0 reactions 0 assignees View on GitHub
Dominant language
Python
Stars
14.9k
Forks
2.9k
PR merge metrics
No merged PRs in 30d

Description

The traceback is as follows:
```

> I1130 17:22:33.347284 140275321640768 run_docker.py:116] Mounting /home/a22/alphafold/project/6y4f -> /mnt/fasta_path_0
> I1130 17:22:33.365633 140275321640768 run_docker.py:116] Mounting /home/a22/afdata/uniref90 -> /mnt/uniref90_database_path
> I1130 17:22:33.369917 140275321640768 run_docker.py:116] Mounting /home/a22/afdata/mgnify -> /mnt/mgnify_database_path
> I1130 17:22:33.370005 140275321640768 run_docker.py:116] Mounting /home/a22/afdata -> /mnt/data_dir
> I1130 17:22:33.383804 140275321640768 run_docker.py:116] Mounting /home/a22/afdata/pdb_mmcif/mmcif_files -> /mnt/template_mmcif_dir
> I1130 17:22:33.394144 140275321640768 run_docker.py:116] Mounting /home/a22/afdata/pdb_mmcif -> /mnt/obsolete_pdbs_path
> I1130 17:22:33.408813 140275321640768 run_docker.py:116] Mounting /home/a22/afdata/pdb70 -> /mnt/pdb70_database_path
> I1130 17:22:33.415395 140275321640768 run_docker.py:116] Mounting /home/a22/afdata/uniref30 -> /mnt/uniref30_database_path
> I1130 17:22:33.424955 140275321640768 run_docker.py:116] Mounting /home/a22/afdata/bfd -> /mnt/bfd_database_path
> Traceback (most recent call last):
> File "/home/a22/anaconda3/envs/alphafold2-docker/lib/python3.11/site-packages/docker/api/client.py", line 214, in _retrieve_server_version
> return self.version(api_version=False)["ApiVersion"]
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> File "/home/a22/anaconda3/envs/alphafold2-docker/lib/python3.11/site-packages/docker/api/daemon.py", line 181, in version
> return self._result(self._get(url), json=True)
> ^^^^^^^^^^^^^^
> File "/home/a22/anaconda3/envs/alphafold2-docker/lib/python3.11/site-packages/docker/utils/decorators.py", line 46, in inner
> return f(self, *args, **kwargs)
> ^^^^^^^^^^^^^^^^^^^^^^^^
> File "/home/a22/anaconda3/envs/alphafold2-docker/lib/python3.11/site-packages/docker/api/client.py", line 237, in _get return self.get(url, **self._set_request_timeout(kwargs))
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> File "/home/a22/anaconda3/envs/alphafold2-docker/lib/python3.11/site-packages/requests/sessions.py", line 602, in get
> return self.request("GET", url, **kwargs)
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> File "/home/a22/anaconda3/envs/alphafold2-docker/lib/python3.11/site-packages/requests/sessions.py", line 589, in request
> resp = self.send(prep, **send_kwargs)
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> File "/home/a22/anaconda3/envs/alphafold2-docker/lib/python3.11/site-packages/requests/sessions.py", line 703, in send r = adapter.send(request, **kwargs)
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> File "/home/a22/anaconda3/envs/alphafold2-docker/lib/python3.11/site-packages/requests/adapters.py", line 486, in send resp = conn.urlopen(
> ^^^^^^^^^^^^^
> File "/home/a22/anaconda3/envs/alphafold2-docker/lib/python3.11/site-packages/urllib3/connectionpool.py", line 790, in urlopen
> response = self._make_request(
> ^^^^^^^^^^^^^^^^^^^
> File "/home/a22/anaconda3/envs/alphafold2-docker/lib/python3.11/site-packages/urllib3/connectionpool.py", line 496, in _make_request
> conn.request(
> TypeError: HTTPConnection.request() got an unexpected keyword argument 'chunked'
>
> During handling of the above exception, another exception occurred:
>
> Traceback (most recent call last):
> File "/home/a22/alphafold/docker/run_docker.py", line 267, in
> app.run(main)
> File "/home/a22/anaconda3/envs/alphafold2-docker/lib/python3.11/site-packages/absl/app.py", line 312, in run
> _run_main(main, args)
> File "/home/a22/anaconda3/envs/alphafold2-docker/lib/python3.11/site-packages/absl/app.py", line 258, in _run_main
> sys.exit(main(argv))
> ^^^^^^^^^^
> File "/home/a22/alphafold/docker/run_docker.py", line 232, in main
> client = docker.from_env()
> ^^^^^^^^^^^^^^^^^
> File "/home/a22/anaconda3/envs/alphafold2-docker/lib/python3.11/site-packages/docker/client.py", line 96, in from_env
> return cls(
> ^^^^
> File "/home/a22/anaconda3/envs/alphafold2-docker/lib/python3.11/site-packages/docker/client.py", line 45, in __init__
> self.api = APIClient(*args, **kwargs)
> ^^^^^^^^^^^^^^^^^^^^^^^^^^
> File "/home/a22/anaconda3/envs/alphafold2-docker/lib/python3.11/site-packages/docker/api/client.py", line 197, in __init__
> self._version = self._retrieve_server_version()
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> File "/home/a22/anaconda3/envs/alphafold2-docker/lib/python3.11/site-packages/docker/api/client.py", line 221, in _retrieve_server_version
> raise DockerException(
> docker.errors.DockerException: Error while fetching server API version: HTTPConnection.request() got an unexpected keyword argument 'chunked'
```

my environment is as follows:
windows11-WSL2-ubuntu22.04,anaconda 23.7.4, docker-for wsl 4.25.0,NVIDIA 4090,cuda12.2
conda list:
```

# packages in environment at /home/a22/anaconda3/envs/alphafold2-docker:
#
# Name Version Build Channel
_libgcc_mutex 0.1 main defaults
_openmp_mutex 5.1 1_gnu defaults
absl-py 1.0.0 pypi_0 pypi
bzip2 1.0.8 h7b6447c_0 defaults
ca-certificates 2023.08.22 h06a4308_0 defaults
certifi 2023.11.17 pypi_0 pypi
charset-normalizer 3.3.2 pypi_0 pypi
docker 5.0.0 pypi_0 pypi
idna 3.6 pypi_0 pypi
ld_impl_linux-64 2.38 h1181459_1 defaults
libffi 3.4.4 h6a678d5_0 defaults
libgcc-ng 11.2.0 h1234567_1 defaults
libgomp 11.2.0 h1234567_1 defaults
libstdcxx-ng 11.2.0 h1234567_1 defaults
libuuid 1.41.5 h5eee18b_0 defaults
ncurses 6.4 h6a678d5_0 defaults
openssl 3.0.12 h7f8727e_0 defaults
pip 23.3.1 py311h06a4308_0 defaults
python 3.11.5 h955ad1f_0 defaults
readline 8.2 h5eee18b_0 defaults
requests 2.31.0 pypi_0 pypi
setuptools 68.0.0 py311h06a4308_0 defaults
six 1.16.0 pypi_0 pypi
sqlite 3.41.2 h5eee18b_0 defaults
tk 8.6.12 h1ccaba5_0 defaults
tzdata 2023c h04d1e81_0 defaults
urllib3 2.1.0 pypi_0 pypi
websocket-client 1.6.4 pypi_0 pypi
wheel 0.41.2 py311h06a4308_0 defaults
xz 5.4.2 h5eee18b_0 defaults
zlib 1.2.13 h5eee18b_0 defaults

```

```
(alphafold2-docker) a22@C10H15N:~/alphafold$ docker-compose version
Docker Compose version v2.23.0-desktop.1
```

Contributor guide

Open the contributing guide

Assessment

This issue has not been assessed yet.

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.