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nipreps / qkay

Manager for the quality assessment of large neuroimaging studies
Apache License 2.0
4 stars 3 forks source link

Cannot docker-compose up #15

Closed celprov closed 5 months ago

celprov commented 1 year ago

What happened?

When I try to launch q'kay with docker-compose up I get Permission denied error.

So I thought let's launch it with sudo sudo docker-compose up, but then I'm getting another error. Not sure if that error is related to trying to launch it with sudo or because of another bug.

What command did you use?

`docker-compose up`

What version of the software are you running?

latest github main

How are you running this software?

Docker

Is your data BIDS valid?

Yes

Are you reusing any previously computed results?

No

Please copy and paste any relevant log output.

(base) cprovins@hos74379:~/code/qkay$ docker-compose up
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 699, in urlopen
    httplib_response = self._make_request(
  File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 394, in _make_request
    conn.request(method, url, **httplib_request_kw)
  File "/usr/lib/python3.10/http/client.py", line 1282, in request
    self._send_request(method, url, body, headers, encode_chunked)
  File "/usr/lib/python3.10/http/client.py", line 1328, in _send_request
    self.endheaders(body, encode_chunked=encode_chunked)
  File "/usr/lib/python3.10/http/client.py", line 1277, in endheaders
    self._send_output(message_body, encode_chunked=encode_chunked)
  File "/usr/lib/python3.10/http/client.py", line 1037, in _send_output
    self.send(msg)
  File "/usr/lib/python3.10/http/client.py", line 975, in send
    self.connect()
  File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 30, in connect
    sock.connect(self.unix_socket)
PermissionError: [Errno 13] Permission denied

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/requests/adapters.py", line 439, in send
    resp = conn.urlopen(
  File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 755, in urlopen
    retries = retries.increment(
  File "/usr/lib/python3/dist-packages/urllib3/util/retry.py", line 532, in increment
    raise six.reraise(type(error), error, _stacktrace)
  File "/usr/lib/python3/dist-packages/six.py", line 718, in reraise
    raise value.with_traceback(tb)
  File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 699, in urlopen
    httplib_response = self._make_request(
  File "/usr/lib/python3/dist-packages/urllib3/connectionpool.py", line 394, in _make_request
    conn.request(method, url, **httplib_request_kw)
  File "/usr/lib/python3.10/http/client.py", line 1282, in request
    self._send_request(method, url, body, headers, encode_chunked)
  File "/usr/lib/python3.10/http/client.py", line 1328, in _send_request
    self.endheaders(body, encode_chunked=encode_chunked)
  File "/usr/lib/python3.10/http/client.py", line 1277, in endheaders
    self._send_output(message_body, encode_chunked=encode_chunked)
  File "/usr/lib/python3.10/http/client.py", line 1037, in _send_output
    self.send(msg)
  File "/usr/lib/python3.10/http/client.py", line 975, in send
    self.connect()
  File "/usr/lib/python3/dist-packages/docker/transport/unixconn.py", line 30, in connect
    sock.connect(self.unix_socket)
urllib3.exceptions.ProtocolError: ('Connection aborted.', PermissionError(13, 'Permission denied'))

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/docker/api/client.py", line 214, in _retrieve_server_version
    return self.version(api_version=False)["ApiVersion"]
  File "/usr/lib/python3/dist-packages/docker/api/daemon.py", line 181, in version
    return self._result(self._get(url), json=True)
  File "/usr/lib/python3/dist-packages/docker/utils/decorators.py", line 46, in inner
    return f(self, *args, **kwargs)
  File "/usr/lib/python3/dist-packages/docker/api/client.py", line 237, in _get
    return self.get(url, **self._set_request_timeout(kwargs))
  File "/usr/lib/python3/dist-packages/requests/sessions.py", line 557, in get
    return self.request('GET', url, **kwargs)
  File "/usr/lib/python3/dist-packages/requests/sessions.py", line 544, in request
    resp = self.send(prep, **send_kwargs)
  File "/usr/lib/python3/dist-packages/requests/sessions.py", line 657, in send
    r = adapter.send(request, **kwargs)
  File "/usr/lib/python3/dist-packages/requests/adapters.py", line 498, in send
    raise ConnectionError(err, request=request)
requests.exceptions.ConnectionError: ('Connection aborted.', PermissionError(13, 'Permission denied'))

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/bin/docker-compose", line 33, in <module>
    sys.exit(load_entry_point('docker-compose==1.29.2', 'console_scripts', 'docker-compose')())
  File "/usr/lib/python3/dist-packages/compose/cli/main.py", line 81, in main
    command_func()
  File "/usr/lib/python3/dist-packages/compose/cli/main.py", line 200, in perform_command
    project = project_from_options('.', options)
  File "/usr/lib/python3/dist-packages/compose/cli/command.py", line 60, in project_from_options
    return get_project(
  File "/usr/lib/python3/dist-packages/compose/cli/command.py", line 152, in get_project
    client = get_client(
  File "/usr/lib/python3/dist-packages/compose/cli/docker_client.py", line 41, in get_client
    client = docker_client(
  File "/usr/lib/python3/dist-packages/compose/cli/docker_client.py", line 170, in docker_client
    client = APIClient(use_ssh_client=not use_paramiko_ssh, **kwargs)
  File "/usr/lib/python3/dist-packages/docker/api/client.py", line 197, in __init__
    self._version = self._retrieve_server_version()
  File "/usr/lib/python3/dist-packages/docker/api/client.py", line 221, in _retrieve_server_version
    raise DockerException(
docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', PermissionError(13, 'Permission denied'))
(base) cprovins@hos74379:~/code/qkay$ sudo docker-compose up
Creating qkay_db_1 ... error

ERROR: for qkay_db_1  Cannot create container for service db: invalid volume specification: 'qkay_db-data:.:rw': invalid mount config for type "volume": invalid mount path: '.' mount path must be absolute

ERROR: for db  Cannot create container for service db: invalid volume specification: 'qkay_db-data:.:rw': invalid mount config for type "volume": invalid mount path: '.' mount path must be absolute
ERROR: Encountered errors while bringing up the project.
(base) cprovins@hos74379:~/code/qkay$

Additional information / screenshots

No response

esavary commented 5 months ago

Docker requires sudo for non-root users, but you can follow these steps (https://docs.docker.com/engine/install/linux-postinstall/) to use Docker without typing sudo each time. Are you still experiencing the second error with the updated code? I did not manage to reproduce it on my computer.

celprov commented 5 months ago

No I did not run into this error since the first time I posted it.

esavary commented 5 months ago

Great news! I'll close the issue but feel free to reopen it if you encounter the error again