google-deepmind / google-deepmind/alphafold
docker.errors.DockerException: Error while fetching server API version: Not supported URL scheme http+docker
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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
`
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