google-deepmind / google-deepmind/alphafold

docker.errors.DockerException: Error while fetching server API version: Not supported URL scheme http+docker

Open
#1,066 4 comments 1 reaction 0 assignees View on GitHub
Dominant language
Python
Stars
14.9k
Forks
2.9k
PR merge metrics
No merged PRs in 30d

Description

I've been trying to get my installation working again after upgrading to Ubuntu 24.04 Noble.

Running with either my old docker image or a new one built using Ross Walker's updated Dockerfile from https://github.com/google-deepmind/alphafold/issues/945 results in the following:

`I0204 10:07:10.296046 136820828736384 run_docker.py:116] Mounting /home/obarker/IRF4/N-term -> /mnt/fasta_path_0
I0204 10:07:10.296793 136820828736384 run_docker.py:116] Mounting /home/apps/alphafold2/AF_Data/uniref90 -> /mnt/uniref90_database_path
I0204 10:07:10.297129 136820828736384 run_docker.py:116] Mounting /home/apps/alphafold2/AF_Data/mgnify -> /mnt/mgnify_database_path
I0204 10:07:10.297229 136820828736384 run_docker.py:116] Mounting /home/apps/alphafold2/AF_Data -> /mnt/data_dir
I0204 10:07:10.297310 136820828736384 run_docker.py:116] Mounting /home/apps/alphafold2/AF_Data/pdb_mmcif/mmcif_files -> /mnt/template_mmcif_dir
I0204 10:07:10.297717 136820828736384 run_docker.py:116] Mounting /home/apps/alphafold2/AF_Data/pdb_mmcif -> /mnt/obsolete_pdbs_path
I0204 10:07:10.298088 136820828736384 run_docker.py:116] Mounting /home/apps/alphafold2/AF_Data/pdb70 -> /mnt/pdb70_database_path
I0204 10:07:10.298490 136820828736384 run_docker.py:116] Mounting /home/apps/alphafold2/AF_Data/uniref30 -> /mnt/uniref30_database_path
I0204 10:07:10.298912 136820828736384 run_docker.py:116] Mounting /home/apps/alphafold2/AF_Data/bfd -> /mnt/bfd_database_path
Traceback (most recent call last):
File "/home/apps/alphafold2/af2/lib/python3.11/site-packages/requests/adapters.py", line 633, in send
conn = self.get_connection_with_tls_context(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/apps/alphafold2/af2/lib/python3.11/site-packages/requests/adapters.py", line 489, in get_connection_with_tls_context
conn = self.poolmanager.connection_from_host(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/apps/alphafold2/af2/lib/python3.11/site-packages/urllib3/poolmanager.py", line 303, in connection_from_host
return self.connection_from_context(request_context)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/apps/alphafold2/af2/lib/python3.11/site-packages/urllib3/poolmanager.py", line 325, in connection_from_context
raise URLSchemeUnknown(scheme)
urllib3.exceptions.URLSchemeUnknown: Not supported URL scheme http+docker

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/apps/alphafold2/af2/lib/python3.11/site-packages/docker/api/client.py", line 214, in _retrieve_server_version
return self.version(api_version=False)["ApiVersion"]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/apps/alphafold2/af2/lib/python3.11/site-packages/docker/api/daemon.py", line 181, in version
return self._result(self._get(url), json=True)
^^^^^^^^^^^^^^
File "/home/apps/alphafold2/af2/lib/python3.11/site-packages/docker/utils/decorators.py", line 46, in inner
return f(self, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/apps/alphafold2/af2/lib/python3.11/site-packages/docker/api/client.py", line 237, in _get
return self.get(url, **self._set_request_timeout(kwargs))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/apps/alphafold2/af2/lib/python3.11/site-packages/requests/sessions.py", line 602, in get
return self.request("GET", url, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/apps/alphafold2/af2/lib/python3.11/site-packages/requests/sessions.py", line 589, in request
resp = self.send(prep, **send_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/apps/alphafold2/af2/lib/python3.11/site-packages/requests/sessions.py", line 703, in send
r = adapter.send(request, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/apps/alphafold2/af2/lib/python3.11/site-packages/requests/adapters.py", line 637, in send
raise InvalidURL(e, request=request)
requests.exceptions.InvalidURL: Not supported URL scheme http+docker

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/apps/alphafold2/alphafold/docker/run_docker.py", line 267, in
app.run(main)
File "/home/apps/alphafold2/af2/lib/python3.11/site-packages/absl/app.py", line 312, in run
_run_main(main, args)
File "/home/apps/alphafold2/af2/lib/python3.11/site-packages/absl/app.py", line 258, in _run_main
sys.exit(main(argv))
^^^^^^^^^^
File "/home/apps/alphafold2/alphafold/docker/run_docker.py", line 232, in main
client = docker.from_env()
^^^^^^^^^^^^^^^^^
File "/home/apps/alphafold2/af2/lib/python3.11/site-packages/docker/client.py", line 96, in from_env
return cls(
^^^^
File "/home/apps/alphafold2/af2/lib/python3.11/site-packages/docker/client.py", line 45, in __init__
self.api = APIClient(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/apps/alphafold2/af2/lib/python3.11/site-packages/docker/api/client.py", line 197, in __init__
self._version = self._retrieve_server_version()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/apps/alphafold2/af2/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: Not supported URL scheme http+docker`

Docker appears to be installed (27.1.1) and working OK (hello-world works fine at least)

`Client: Docker Engine - Community
Version: 27.1.1
API version: 1.46
Go version: go1.21.12
Git commit: 6312585
Built: Tue Jul 23 19:56:46 2024
OS/Arch: linux/amd64
Context: default

Server: Docker Engine - Community
Engine:
Version: 27.1.1
API version: 1.46 (minimum version 1.24)
Go version: go1.21.12
Git commit: cc13f95
Built: Tue Jul 23 19:56:46 2024
OS/Arch: linux/amd64
Experimental: false
containerd:
Version: 1.7.19
GitCommit: 2bf793ef6dc9a18e00cb12efb64355c2c9d5eb41
runc:
Version: 1.7.19
GitCommit: v1.1.13-0-g58aa920
docker-init:
Version: 0.19.0
GitCommit: de40ad0
`

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.