Skip to content

Instantly share code, notes, and snippets.

@erikbgithub

erikbgithub/gist:be8bbcef26b01d3c77890ebb714857d7

Created October 1, 2021 14:06
Show Gist options
  • Star 0 You must be signed in to star a gist
  • Fork 0 You must be signed in to fork a gist
  • Save erikbgithub/be8bbcef26b01d3c77890ebb714857d7 to your computer and use it in GitHub Desktop.
Save erikbgithub/be8bbcef26b01d3c77890ebb714857d7 to your computer and use it in GitHub Desktop.
Download ZIP
Raw
gistfile1.txt
2021-10-01 13:59:01.451 tests.test_4taskrun.TestTaskRunner.test_runtime_memory.t:nop ERROR task nop ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_0uyaw6tp/20211001_135901_nop", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:59:01.451 tests.test_4taskrun.TestTaskRunner.test_runtime_memory.t:nop ERROR task nop ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_0uyaw6tp/20211001_135901_nop", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:58:57.995 tests.test_4taskrun.TestTaskRunner.test_errors.t:t ERROR task t ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_0y8msvie/20211001_135857_t", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:58:57.995 tests.test_4taskrun.TestTaskRunner.test_errors.t:t ERROR task t ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_0y8msvie/20211001_135857_t", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:58:59.950 tests.test_4taskrun.TestTaskRunner.test_logging_std_err.t:std_err_log_check NOTICE task start :: name: "std_err_log_check", source: "", line: 3, column: 9, dir: "/tmp/miniwdl_test_taskrun_1j6t3kki/20211001_135859_std_err_log_check", thread: 140007104997184
2021-10-01 13:58:59.950 tests.test_4taskrun.TestTaskRunner.test_logging_std_err.t:std_err_log_check.CallCache.FlockHolder DEBUG flock :: file: "/tmp/miniwdl_test_taskrun_1j6t3kki/20211001_135859_std_err_log_check/task.log", realpath: "/tmp/miniwdl_test_taskrun_1j6t3kki/20211001_135859_std_err_log_check/task.log", exclusive: true, wait: false
2021-10-01 13:58:59.950 tests.test_4taskrun.TestTaskRunner.test_logging_std_err.t:std_err_log_check.CallCache.FlockHolder DEBUG flocked :: file: "/tmp/miniwdl_test_taskrun_1j6t3kki/20211001_135859_std_err_log_check/task.log", realpath: "/tmp/miniwdl_test_taskrun_1j6t3kki/20211001_135859_std_err_log_check/task.log", exclusive: true, name_inode: 471, fd_inode: 471
2021-10-01 13:58:59.977 tests.test_4taskrun.TestTaskRunner.test_logging_std_err.t:std_err_log_check DEBUG Traceback (most recent call last):
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 706, in urlopen
chunked=chunked,
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 394, in _make_request
conn.request(method, url, **httplib_request_kw)
File "/usr/lib/python3.6/http/client.py", line 1281, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1327, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1276, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1042, in _send_output
self.send(msg)
File "/usr/lib/python3.6/http/client.py", line 980, in send
self.connect()
File "/home/wdler/.local/lib/python3.6/site-packages/docker/transport/unixconn.py", line 30, in connect
sock.connect(self.unix_socket)
FileNotFoundError: [Errno 2] No such file or directory
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/wdler/.local/lib/python3.6/site-packages/requests/adapters.py", line 449, in send
timeout=timeout
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 756, in urlopen
method, url, error=e, _pool=self, _stacktrace=sys.exc_info()[2]
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/util/retry.py", line 532, in increment
raise six.reraise(type(error), error, _stacktrace)
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/packages/six.py", line 769, in reraise
raise value.with_traceback(tb)
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 706, in urlopen
chunked=chunked,
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 394, in _make_request
conn.request(method, url, **httplib_request_kw)
File "/usr/lib/python3.6/http/client.py", line 1281, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1327, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1276, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1042, in _send_output
self.send(msg)
File "/usr/lib/python3.6/http/client.py", line 980, in send
self.connect()
File "/home/wdler/.local/lib/python3.6/site-packages/docker/transport/unixconn.py", line 30, in connect
sock.connect(self.unix_socket)
urllib3.exceptions.ProtocolError: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/wdler/.local/lib/python3.6/site-packages/docker/api/client.py", line 214, in _retrieve_server_version
return self.version(api_version=False)["ApiVersion"]
File "/home/wdler/.local/lib/python3.6/site-packages/docker/api/daemon.py", line 181, in version
return self._result(self._get(url), json=True)
File "/home/wdler/.local/lib/python3.6/site-packages/docker/utils/decorators.py", line 46, in inner
return f(self, *args, **kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/docker/api/client.py", line 237, in _get
return self.get(url, **self._set_request_timeout(kwargs))
File "/home/wdler/.local/lib/python3.6/site-packages/requests/sessions.py", line 555, in get
return self.request('GET', url, **kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/requests/sessions.py", line 542, in request
resp = self.send(prep, **send_kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/requests/sessions.py", line 655, in send
r = adapter.send(request, **kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/requests/adapters.py", line 498, in send
raise ConnectionError(err, request=request)
requests.exceptions.ConnectionError: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/wdler/miniwdl/WDL/runtime/task.py", line 164, in run_local_task
container = new_task_container(cfg, logger, run_id, run_dir)
File "/home/wdler/miniwdl/WDL/runtime/task_container.py", line 384, in new
backend_cls.global_init(cfg, logger)
File "/home/wdler/miniwdl/WDL/runtime/task_container.py", line 400, in global_init
client = docker.from_env(version="auto")
File "/home/wdler/.local/lib/python3.6/site-packages/docker/client.py", line 101, in from_env
**kwargs_from_env(**kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/docker/client.py", line 45, in __init__
self.api = APIClient(*args, **kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/docker/api/client.py", line 197, in __init__
self._version = self._retrieve_server_version()
File "/home/wdler/.local/lib/python3.6/site-packages/docker/api/client.py", line 222, in _retrieve_server_version
f'Error while fetching server API version: {e}'
docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))
2021-10-01 13:58:59.977 tests.test_4taskrun.TestTaskRunner.test_logging_std_err.t:std_err_log_check ERROR task std_err_log_check ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_1j6t3kki/20211001_135859_std_err_log_check", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:58:59.978 tests.test_4taskrun.TestTaskRunner.test_logging_std_err.t:std_err_log_check.CallCache.FlockHolder DEBUG close :: file: "/tmp/miniwdl_test_taskrun_1j6t3kki/20211001_135859_std_err_log_check/task.log", exclusive: true
2021-10-01 13:58:59.950 tests.test_4taskrun.TestTaskRunner.test_logging_std_err.t:std_err_log_check NOTICE task start :: name: "std_err_log_check", source: "", line: 3, column: 9, dir: "/tmp/miniwdl_test_taskrun_1j6t3kki/20211001_135859_std_err_log_check", thread: 140007104997184
2021-10-01 13:58:59.950 tests.test_4taskrun.TestTaskRunner.test_logging_std_err.t:std_err_log_check.CallCache.FlockHolder DEBUG flock :: file: "/tmp/miniwdl_test_taskrun_1j6t3kki/20211001_135859_std_err_log_check/task.log", realpath: "/tmp/miniwdl_test_taskrun_1j6t3kki/20211001_135859_std_err_log_check/task.log", exclusive: true, wait: false
2021-10-01 13:58:59.950 tests.test_4taskrun.TestTaskRunner.test_logging_std_err.t:std_err_log_check.CallCache.FlockHolder DEBUG flocked :: file: "/tmp/miniwdl_test_taskrun_1j6t3kki/20211001_135859_std_err_log_check/task.log", realpath: "/tmp/miniwdl_test_taskrun_1j6t3kki/20211001_135859_std_err_log_check/task.log", exclusive: true, name_inode: 471, fd_inode: 471
2021-10-01 13:58:59.977 tests.test_4taskrun.TestTaskRunner.test_logging_std_err.t:std_err_log_check DEBUG Traceback (most recent call last):
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 706, in urlopen
chunked=chunked,
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 394, in _make_request
conn.request(method, url, **httplib_request_kw)
File "/usr/lib/python3.6/http/client.py", line 1281, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1327, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1276, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1042, in _send_output
self.send(msg)
File "/usr/lib/python3.6/http/client.py", line 980, in send
self.connect()
File "/home/wdler/.local/lib/python3.6/site-packages/docker/transport/unixconn.py", line 30, in connect
sock.connect(self.unix_socket)
FileNotFoundError: [Errno 2] No such file or directory
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/wdler/.local/lib/python3.6/site-packages/requests/adapters.py", line 449, in send
timeout=timeout
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 756, in urlopen
method, url, error=e, _pool=self, _stacktrace=sys.exc_info()[2]
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/util/retry.py", line 532, in increment
raise six.reraise(type(error), error, _stacktrace)
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/packages/six.py", line 769, in reraise
raise value.with_traceback(tb)
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 706, in urlopen
chunked=chunked,
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 394, in _make_request
conn.request(method, url, **httplib_request_kw)
File "/usr/lib/python3.6/http/client.py", line 1281, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1327, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1276, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1042, in _send_output
self.send(msg)
File "/usr/lib/python3.6/http/client.py", line 980, in send
self.connect()
File "/home/wdler/.local/lib/python3.6/site-packages/docker/transport/unixconn.py", line 30, in connect
sock.connect(self.unix_socket)
urllib3.exceptions.ProtocolError: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/wdler/.local/lib/python3.6/site-packages/docker/api/client.py", line 214, in _retrieve_server_version
return self.version(api_version=False)["ApiVersion"]
File "/home/wdler/.local/lib/python3.6/site-packages/docker/api/daemon.py", line 181, in version
return self._result(self._get(url), json=True)
File "/home/wdler/.local/lib/python3.6/site-packages/docker/utils/decorators.py", line 46, in inner
return f(self, *args, **kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/docker/api/client.py", line 237, in _get
return self.get(url, **self._set_request_timeout(kwargs))
File "/home/wdler/.local/lib/python3.6/site-packages/requests/sessions.py", line 555, in get
return self.request('GET', url, **kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/requests/sessions.py", line 542, in request
resp = self.send(prep, **send_kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/requests/sessions.py", line 655, in send
r = adapter.send(request, **kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/requests/adapters.py", line 498, in send
raise ConnectionError(err, request=request)
requests.exceptions.ConnectionError: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/wdler/miniwdl/WDL/runtime/task.py", line 164, in run_local_task
container = new_task_container(cfg, logger, run_id, run_dir)
File "/home/wdler/miniwdl/WDL/runtime/task_container.py", line 384, in new
backend_cls.global_init(cfg, logger)
File "/home/wdler/miniwdl/WDL/runtime/task_container.py", line 400, in global_init
client = docker.from_env(version="auto")
File "/home/wdler/.local/lib/python3.6/site-packages/docker/client.py", line 101, in from_env
**kwargs_from_env(**kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/docker/client.py", line 45, in __init__
self.api = APIClient(*args, **kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/docker/api/client.py", line 197, in __init__
self._version = self._retrieve_server_version()
File "/home/wdler/.local/lib/python3.6/site-packages/docker/api/client.py", line 222, in _retrieve_server_version
f'Error while fetching server API version: {e}'
docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))
2021-10-01 13:58:59.977 tests.test_4taskrun.TestTaskRunner.test_logging_std_err.t:std_err_log_check ERROR task std_err_log_check ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_1j6t3kki/20211001_135859_std_err_log_check", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:58:59.978 tests.test_4taskrun.TestTaskRunner.test_logging_std_err.t:std_err_log_check.CallCache.FlockHolder DEBUG close :: file: "/tmp/miniwdl_test_taskrun_1j6t3kki/20211001_135859_std_err_log_check/task.log", exclusive: true
2021-10-01 13:59:03.664 tests.test_4taskrun.TestTaskRunner.test_write_lines.t:hello_friends ERROR task hello_friends ( Ln 3 Col 13) failed :: dir: "/tmp/miniwdl_test_taskrun_5v116g6v/20211001_135903_hello_friends", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:59:03.664 tests.test_4taskrun.TestTaskRunner.test_write_lines.t:hello_friends ERROR task hello_friends ( Ln 3 Col 13) failed :: dir: "/tmp/miniwdl_test_taskrun_5v116g6v/20211001_135903_hello_friends", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:59:03.450 tests.test_4taskrun.TestTaskRunner.test_workdir_ownership.t:clobber ERROR task clobber ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_791abico/20211001_135903_clobber", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:59:03.450 tests.test_4taskrun.TestTaskRunner.test_workdir_ownership.t:clobber ERROR task clobber ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_791abico/20211001_135903_clobber", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:59:01.621 tests.test_4taskrun.TestTaskRunner.test_runtime_memory_limit.t:limit ERROR task limit ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun__wf5rcnp/20211001_135901_limit", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:59:01.621 tests.test_4taskrun.TestTaskRunner.test_runtime_memory_limit.t:limit ERROR task limit ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun__wf5rcnp/20211001_135901_limit", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:59:00.232 tests.test_4taskrun.TestTaskRunner.test_logging_std_err_captures_full_line.t:std_err_log_check NOTICE task start :: name: "std_err_log_check", source: "", line: 3, column: 17, dir: "/tmp/miniwdl_test_taskrun_drfzd6r4/20211001_135900_std_err_log_check", thread: 140007104997184
2021-10-01 13:59:00.232 tests.test_4taskrun.TestTaskRunner.test_logging_std_err_captures_full_line.t:std_err_log_check.CallCache.FlockHolder DEBUG flock :: file: "/tmp/miniwdl_test_taskrun_drfzd6r4/20211001_135900_std_err_log_check/task.log", realpath: "/tmp/miniwdl_test_taskrun_drfzd6r4/20211001_135900_std_err_log_check/task.log", exclusive: true, wait: false
2021-10-01 13:59:00.232 tests.test_4taskrun.TestTaskRunner.test_logging_std_err_captures_full_line.t:std_err_log_check.CallCache.FlockHolder DEBUG flocked :: file: "/tmp/miniwdl_test_taskrun_drfzd6r4/20211001_135900_std_err_log_check/task.log", realpath: "/tmp/miniwdl_test_taskrun_drfzd6r4/20211001_135900_std_err_log_check/task.log", exclusive: true, name_inode: 493, fd_inode: 493
2021-10-01 13:59:00.249 tests.test_4taskrun.TestTaskRunner.test_logging_std_err_captures_full_line.t:std_err_log_check DEBUG Traceback (most recent call last):
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 706, in urlopen
chunked=chunked,
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 394, in _make_request
conn.request(method, url, **httplib_request_kw)
File "/usr/lib/python3.6/http/client.py", line 1281, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1327, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1276, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1042, in _send_output
self.send(msg)
File "/usr/lib/python3.6/http/client.py", line 980, in send
self.connect()
File "/home/wdler/.local/lib/python3.6/site-packages/docker/transport/unixconn.py", line 30, in connect
sock.connect(self.unix_socket)
FileNotFoundError: [Errno 2] No such file or directory
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/wdler/.local/lib/python3.6/site-packages/requests/adapters.py", line 449, in send
timeout=timeout
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 756, in urlopen
method, url, error=e, _pool=self, _stacktrace=sys.exc_info()[2]
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/util/retry.py", line 532, in increment
raise six.reraise(type(error), error, _stacktrace)
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/packages/six.py", line 769, in reraise
raise value.with_traceback(tb)
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 706, in urlopen
chunked=chunked,
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 394, in _make_request
conn.request(method, url, **httplib_request_kw)
File "/usr/lib/python3.6/http/client.py", line 1281, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1327, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1276, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1042, in _send_output
self.send(msg)
File "/usr/lib/python3.6/http/client.py", line 980, in send
self.connect()
File "/home/wdler/.local/lib/python3.6/site-packages/docker/transport/unixconn.py", line 30, in connect
sock.connect(self.unix_socket)
urllib3.exceptions.ProtocolError: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/wdler/.local/lib/python3.6/site-packages/docker/api/client.py", line 214, in _retrieve_server_version
return self.version(api_version=False)["ApiVersion"]
File "/home/wdler/.local/lib/python3.6/site-packages/docker/api/daemon.py", line 181, in version
return self._result(self._get(url), json=True)
File "/home/wdler/.local/lib/python3.6/site-packages/docker/utils/decorators.py", line 46, in inner
return f(self, *args, **kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/docker/api/client.py", line 237, in _get
return self.get(url, **self._set_request_timeout(kwargs))
File "/home/wdler/.local/lib/python3.6/site-packages/requests/sessions.py", line 555, in get
return self.request('GET', url, **kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/requests/sessions.py", line 542, in request
resp = self.send(prep, **send_kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/requests/sessions.py", line 655, in send
r = adapter.send(request, **kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/requests/adapters.py", line 498, in send
raise ConnectionError(err, request=request)
requests.exceptions.ConnectionError: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/wdler/miniwdl/WDL/runtime/task.py", line 164, in run_local_task
container = new_task_container(cfg, logger, run_id, run_dir)
File "/home/wdler/miniwdl/WDL/runtime/task_container.py", line 384, in new
backend_cls.global_init(cfg, logger)
File "/home/wdler/miniwdl/WDL/runtime/task_container.py", line 400, in global_init
client = docker.from_env(version="auto")
File "/home/wdler/.local/lib/python3.6/site-packages/docker/client.py", line 101, in from_env
**kwargs_from_env(**kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/docker/client.py", line 45, in __init__
self.api = APIClient(*args, **kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/docker/api/client.py", line 197, in __init__
self._version = self._retrieve_server_version()
File "/home/wdler/.local/lib/python3.6/site-packages/docker/api/client.py", line 222, in _retrieve_server_version
f'Error while fetching server API version: {e}'
docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))
2021-10-01 13:59:00.249 tests.test_4taskrun.TestTaskRunner.test_logging_std_err_captures_full_line.t:std_err_log_check ERROR task std_err_log_check ( Ln 3 Col 17) failed :: dir: "/tmp/miniwdl_test_taskrun_drfzd6r4/20211001_135900_std_err_log_check", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:59:00.249 tests.test_4taskrun.TestTaskRunner.test_logging_std_err_captures_full_line.t:std_err_log_check.CallCache.FlockHolder DEBUG close :: file: "/tmp/miniwdl_test_taskrun_drfzd6r4/20211001_135900_std_err_log_check/task.log", exclusive: true
2021-10-01 13:59:00.232 tests.test_4taskrun.TestTaskRunner.test_logging_std_err_captures_full_line.t:std_err_log_check NOTICE task start :: name: "std_err_log_check", source: "", line: 3, column: 17, dir: "/tmp/miniwdl_test_taskrun_drfzd6r4/20211001_135900_std_err_log_check", thread: 140007104997184
2021-10-01 13:59:00.232 tests.test_4taskrun.TestTaskRunner.test_logging_std_err_captures_full_line.t:std_err_log_check.CallCache.FlockHolder DEBUG flock :: file: "/tmp/miniwdl_test_taskrun_drfzd6r4/20211001_135900_std_err_log_check/task.log", realpath: "/tmp/miniwdl_test_taskrun_drfzd6r4/20211001_135900_std_err_log_check/task.log", exclusive: true, wait: false
2021-10-01 13:59:00.232 tests.test_4taskrun.TestTaskRunner.test_logging_std_err_captures_full_line.t:std_err_log_check.CallCache.FlockHolder DEBUG flocked :: file: "/tmp/miniwdl_test_taskrun_drfzd6r4/20211001_135900_std_err_log_check/task.log", realpath: "/tmp/miniwdl_test_taskrun_drfzd6r4/20211001_135900_std_err_log_check/task.log", exclusive: true, name_inode: 493, fd_inode: 493
2021-10-01 13:59:00.249 tests.test_4taskrun.TestTaskRunner.test_logging_std_err_captures_full_line.t:std_err_log_check DEBUG Traceback (most recent call last):
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 706, in urlopen
chunked=chunked,
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 394, in _make_request
conn.request(method, url, **httplib_request_kw)
File "/usr/lib/python3.6/http/client.py", line 1281, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1327, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1276, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1042, in _send_output
self.send(msg)
File "/usr/lib/python3.6/http/client.py", line 980, in send
self.connect()
File "/home/wdler/.local/lib/python3.6/site-packages/docker/transport/unixconn.py", line 30, in connect
sock.connect(self.unix_socket)
FileNotFoundError: [Errno 2] No such file or directory
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/wdler/.local/lib/python3.6/site-packages/requests/adapters.py", line 449, in send
timeout=timeout
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 756, in urlopen
method, url, error=e, _pool=self, _stacktrace=sys.exc_info()[2]
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/util/retry.py", line 532, in increment
raise six.reraise(type(error), error, _stacktrace)
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/packages/six.py", line 769, in reraise
raise value.with_traceback(tb)
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 706, in urlopen
chunked=chunked,
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 394, in _make_request
conn.request(method, url, **httplib_request_kw)
File "/usr/lib/python3.6/http/client.py", line 1281, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1327, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1276, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1042, in _send_output
self.send(msg)
File "/usr/lib/python3.6/http/client.py", line 980, in send
self.connect()
File "/home/wdler/.local/lib/python3.6/site-packages/docker/transport/unixconn.py", line 30, in connect
sock.connect(self.unix_socket)
urllib3.exceptions.ProtocolError: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/wdler/.local/lib/python3.6/site-packages/docker/api/client.py", line 214, in _retrieve_server_version
return self.version(api_version=False)["ApiVersion"]
File "/home/wdler/.local/lib/python3.6/site-packages/docker/api/daemon.py", line 181, in version
return self._result(self._get(url), json=True)
File "/home/wdler/.local/lib/python3.6/site-packages/docker/utils/decorators.py", line 46, in inner
return f(self, *args, **kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/docker/api/client.py", line 237, in _get
return self.get(url, **self._set_request_timeout(kwargs))
File "/home/wdler/.local/lib/python3.6/site-packages/requests/sessions.py", line 555, in get
return self.request('GET', url, **kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/requests/sessions.py", line 542, in request
resp = self.send(prep, **send_kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/requests/sessions.py", line 655, in send
r = adapter.send(request, **kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/requests/adapters.py", line 498, in send
raise ConnectionError(err, request=request)
requests.exceptions.ConnectionError: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/wdler/miniwdl/WDL/runtime/task.py", line 164, in run_local_task
container = new_task_container(cfg, logger, run_id, run_dir)
File "/home/wdler/miniwdl/WDL/runtime/task_container.py", line 384, in new
backend_cls.global_init(cfg, logger)
File "/home/wdler/miniwdl/WDL/runtime/task_container.py", line 400, in global_init
client = docker.from_env(version="auto")
File "/home/wdler/.local/lib/python3.6/site-packages/docker/client.py", line 101, in from_env
**kwargs_from_env(**kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/docker/client.py", line 45, in __init__
self.api = APIClient(*args, **kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/docker/api/client.py", line 197, in __init__
self._version = self._retrieve_server_version()
File "/home/wdler/.local/lib/python3.6/site-packages/docker/api/client.py", line 222, in _retrieve_server_version
f'Error while fetching server API version: {e}'
docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))
2021-10-01 13:59:00.249 tests.test_4taskrun.TestTaskRunner.test_logging_std_err_captures_full_line.t:std_err_log_check ERROR task std_err_log_check ( Ln 3 Col 17) failed :: dir: "/tmp/miniwdl_test_taskrun_drfzd6r4/20211001_135900_std_err_log_check", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:59:00.249 tests.test_4taskrun.TestTaskRunner.test_logging_std_err_captures_full_line.t:std_err_log_check.CallCache.FlockHolder DEBUG close :: file: "/tmp/miniwdl_test_taskrun_drfzd6r4/20211001_135900_std_err_log_check/task.log", exclusive: true
2021-10-01 13:58:55.729 tests.test_4taskrun.TestTaskRunner.test_cpu_limit.t:spin ERROR task spin ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_e0h7ggqc/20211001_135855_spin", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:58:55.729 tests.test_4taskrun.TestTaskRunner.test_cpu_limit.t:spin ERROR task spin ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_e0h7ggqc/20211001_135855_spin", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:58:54.626 tests.test_4taskrun.TestTaskRunner.test_command_failure.t:hello ERROR task hello ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_eq8phy8g/20211001_135854_hello", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:58:54.626 tests.test_4taskrun.TestTaskRunner.test_command_failure.t:hello ERROR task hello ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_eq8phy8g/20211001_135854_hello", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:58:59.336 tests.test_4taskrun.TestTaskRunner.test_input_files_rw.t:clobber ERROR task clobber ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_f_438wm2/20211001_135859_clobber", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:58:59.336 tests.test_4taskrun.TestTaskRunner.test_input_files_rw.t:clobber ERROR task clobber ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_f_438wm2/20211001_135859_clobber", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:59:01.050 tests.test_4taskrun.TestTaskRunner.test_orphan_background_process.t:t ERROR task t ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_iv9hvumo/20211001_135901_t", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:59:01.050 tests.test_4taskrun.TestTaskRunner.test_orphan_background_process.t:t ERROR task t ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_iv9hvumo/20211001_135901_t", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:59:01.811 tests.test_4taskrun.TestTaskRunner.test_runtime_returnCodes.t:limit ERROR task limit ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_iy5v20vk/20211001_135901_limit", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:59:01.811 tests.test_4taskrun.TestTaskRunner.test_runtime_returnCodes.t:limit ERROR task limit ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_iy5v20vk/20211001_135901_limit", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:58:56.336 tests.test_4taskrun.TestTaskRunner.test_docker.t:hello ERROR task hello ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_kg3kd1fh/20211001_135856_hello", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:58:56.336 tests.test_4taskrun.TestTaskRunner.test_docker.t:hello ERROR task hello ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_kg3kd1fh/20211001_135856_hello", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:58:58.453 tests.test_4taskrun.TestTaskRunner.test_filename_collisions.t:t ERROR task t ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_ku6gs_g5/20211001_135858_t", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:58:58.453 tests.test_4taskrun.TestTaskRunner.test_filename_collisions.t:t ERROR task t ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_ku6gs_g5/20211001_135858_t", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:59:00.791 tests.test_4taskrun.TestTaskRunner.test_optional_inputs.t:defaults ERROR task defaults ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_m9rdhtw6/20211001_135900_defaults", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:59:00.791 tests.test_4taskrun.TestTaskRunner.test_optional_inputs.t:defaults ERROR task defaults ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_m9rdhtw6/20211001_135900_defaults", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:58:54.041 tests.test_4taskrun.TestTaskRunner.test_coercion.t:t ERROR task t ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_me03c92o/20211001_135853_t", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:58:54.041 tests.test_4taskrun.TestTaskRunner.test_coercion.t:t ERROR task t ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_me03c92o/20211001_135853_t", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:58:56.571 tests.test_4taskrun.TestTaskRunner.test_download_cache.t:lines NOTICE task start :: name: "lines", source: "", line: 3, column: 9, dir: "/tmp/miniwdl_test_taskrun_miumshej/20211001_135856_lines", thread: 140007104997184
2021-10-01 13:58:56.572 tests.test_4taskrun.TestTaskRunner.test_download_cache.t:lines.CallCache.FlockHolder DEBUG flock :: file: "/tmp/miniwdl_test_taskrun_miumshej/20211001_135856_lines/task.log", realpath: "/tmp/miniwdl_test_taskrun_miumshej/20211001_135856_lines/task.log", exclusive: true, wait: false
2021-10-01 13:58:56.572 tests.test_4taskrun.TestTaskRunner.test_download_cache.t:lines.CallCache.FlockHolder DEBUG flocked :: file: "/tmp/miniwdl_test_taskrun_miumshej/20211001_135856_lines/task.log", realpath: "/tmp/miniwdl_test_taskrun_miumshej/20211001_135856_lines/task.log", exclusive: true, name_inode: 281, fd_inode: 281
2021-10-01 13:58:56.623 tests.test_4taskrun.TestTaskRunner.test_download_cache.t:lines INFO download input file :: uri: "https://google.com/robots.txt"
2021-10-01 13:58:56.624 tests.test_4taskrun.TestTaskRunner.test_download_cache.t:lines.CallCache DEBUG no download cache hit :: uri: "https://google.com/robots.txt", cache_path: "/tmp/miniwdl_test_taskrun_miumshej/cache/files/https/google.com/_/robots.txt"
2021-10-01 13:58:56.624 tests.test_4taskrun.TestTaskRunner.test_download_cache.t:lines INFO start download :: uri: "https://google.com/robots.txt"
2021-10-01 13:58:56.642 tests.test_4taskrun.TestTaskRunner.test_download_cache.t:lines.download0.t:download-aria2c NOTICE task start :: name: "aria2c", source: "", line: 2, column: 5, dir: "/tmp/miniwdl_test_taskrun_miumshej/cache/ops/20211001_135856_aria2c", thread: 140007104997184
2021-10-01 13:58:56.643 tests.test_4taskrun.TestTaskRunner.test_download_cache.t:lines.download0.t:download-aria2c.CallCache.FlockHolder DEBUG flock :: file: "/tmp/miniwdl_test_taskrun_miumshej/cache/ops/20211001_135856_aria2c/task.log", realpath: "/tmp/miniwdl_test_taskrun_miumshej/cache/ops/20211001_135856_aria2c/task.log", exclusive: true, wait: false
2021-10-01 13:58:56.644 tests.test_4taskrun.TestTaskRunner.test_download_cache.t:lines.download0.t:download-aria2c.CallCache.FlockHolder DEBUG flocked :: file: "/tmp/miniwdl_test_taskrun_miumshej/cache/ops/20211001_135856_aria2c/task.log", realpath: "/tmp/miniwdl_test_taskrun_miumshej/cache/ops/20211001_135856_aria2c/task.log", exclusive: true, name_inode: 294, fd_inode: 294
2021-10-01 13:58:56.663 tests.test_4taskrun.TestTaskRunner.test_download_cache.t:lines.download0.t:download-aria2c DEBUG Traceback (most recent call last):
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 706, in urlopen
chunked=chunked,
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 394, in _make_request
conn.request(method, url, **httplib_request_kw)
File "/usr/lib/python3.6/http/client.py", line 1281, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1327, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1276, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1042, in _send_output
self.send(msg)
File "/usr/lib/python3.6/http/client.py", line 980, in send
self.connect()
File "/home/wdler/.local/lib/python3.6/site-packages/docker/transport/unixconn.py", line 30, in connect
sock.connect(self.unix_socket)
FileNotFoundError: [Errno 2] No such file or directory
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/wdler/.local/lib/python3.6/site-packages/requests/adapters.py", line 449, in send
timeout=timeout
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 756, in urlopen
method, url, error=e, _pool=self, _stacktrace=sys.exc_info()[2]
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/util/retry.py", line 532, in increment
raise six.reraise(type(error), error, _stacktrace)
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/packages/six.py", line 769, in reraise
raise value.with_traceback(tb)
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 706, in urlopen
chunked=chunked,
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 394, in _make_request
conn.request(method, url, **httplib_request_kw)
File "/usr/lib/python3.6/http/client.py", line 1281, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1327, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1276, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1042, in _send_output
self.send(msg)
File "/usr/lib/python3.6/http/client.py", line 980, in send
self.connect()
File "/home/wdler/.local/lib/python3.6/site-packages/docker/transport/unixconn.py", line 30, in connect
sock.connect(self.unix_socket)
urllib3.exceptions.ProtocolError: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/wdler/.local/lib/python3.6/site-packages/docker/api/client.py", line 214, in _retrieve_server_version
return self.version(api_version=False)["ApiVersion"]
File "/home/wdler/.local/lib/python3.6/site-packages/docker/api/daemon.py", line 181, in version
return self._result(self._get(url), json=True)
File "/home/wdler/.local/lib/python3.6/site-packages/docker/utils/decorators.py", line 46, in inner
return f(self, *args, **kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/docker/api/client.py", line 237, in _get
return self.get(url, **self._set_request_timeout(kwargs))
File "/home/wdler/.local/lib/python3.6/site-packages/requests/sessions.py", line 555, in get
return self.request('GET', url, **kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/requests/sessions.py", line 542, in request
resp = self.send(prep, **send_kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/requests/sessions.py", line 655, in send
r = adapter.send(request, **kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/requests/adapters.py", line 498, in send
raise ConnectionError(err, request=request)
requests.exceptions.ConnectionError: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/wdler/miniwdl/WDL/runtime/task.py", line 164, in run_local_task
container = new_task_container(cfg, logger, run_id, run_dir)
File "/home/wdler/miniwdl/WDL/runtime/task_container.py", line 384, in new
backend_cls.global_init(cfg, logger)
File "/home/wdler/miniwdl/WDL/runtime/task_container.py", line 400, in global_init
client = docker.from_env(version="auto")
File "/home/wdler/.local/lib/python3.6/site-packages/docker/client.py", line 101, in from_env
**kwargs_from_env(**kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/docker/client.py", line 45, in __init__
self.api = APIClient(*args, **kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/docker/api/client.py", line 197, in __init__
self._version = self._retrieve_server_version()
File "/home/wdler/.local/lib/python3.6/site-packages/docker/api/client.py", line 222, in _retrieve_server_version
f'Error while fetching server API version: {e}'
docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))
2021-10-01 13:58:56.663 tests.test_4taskrun.TestTaskRunner.test_download_cache.t:lines.download0.t:download-aria2c ERROR task aria2c ( Ln 2 Col 5) failed :: dir: "/tmp/miniwdl_test_taskrun_miumshej/cache/ops/20211001_135856_aria2c", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:58:56.664 tests.test_4taskrun.TestTaskRunner.test_download_cache.t:lines.download0.t:download-aria2c.CallCache.FlockHolder DEBUG close :: file: "/tmp/miniwdl_test_taskrun_miumshej/cache/ops/20211001_135856_aria2c/task.log", exclusive: true
2021-10-01 13:58:56.665 tests.test_4taskrun.TestTaskRunner.test_download_cache.t:lines DEBUG Traceback (most recent call last):
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 706, in urlopen
chunked=chunked,
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 394, in _make_request
conn.request(method, url, **httplib_request_kw)
File "/usr/lib/python3.6/http/client.py", line 1281, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1327, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1276, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1042, in _send_output
self.send(msg)
File "/usr/lib/python3.6/http/client.py", line 980, in send
self.connect()
File "/home/wdler/.local/lib/python3.6/site-packages/docker/transport/unixconn.py", line 30, in connect
sock.connect(self.unix_socket)
FileNotFoundError: [Errno 2] No such file or directory
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/wdler/.local/lib/python3.6/site-packages/requests/adapters.py", line 449, in send
timeout=timeout
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 756, in urlopen
method, url, error=e, _pool=self, _stacktrace=sys.exc_info()[2]
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/util/retry.py", line 532, in increment
raise six.reraise(type(error), error, _stacktrace)
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/packages/six.py", line 769, in reraise
raise value.with_traceback(tb)
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 706, in urlopen
chunked=chunked,
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 394, in _make_request
conn.request(method, url, **httplib_request_kw)
File "/usr/lib/python3.6/http/client.py", line 1281, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1327, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1276, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1042, in _send_output
self.send(msg)
File "/usr/lib/python3.6/http/client.py", line 980, in send
self.connect()
File "/home/wdler/.local/lib/python3.6/site-packages/docker/transport/unixconn.py", line 30, in connect
sock.connect(self.unix_socket)
urllib3.exceptions.ProtocolError: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/wdler/.local/lib/python3.6/site-packages/docker/api/client.py", line 214, in _retrieve_server_version
return self.version(api_version=False)["ApiVersion"]
File "/home/wdler/.local/lib/python3.6/site-packages/docker/api/daemon.py", line 181, in version
return self._result(self._get(url), json=True)
File "/home/wdler/.local/lib/python3.6/site-packages/docker/utils/decorators.py", line 46, in inner
return f(self, *args, **kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/docker/api/client.py", line 237, in _get
return self.get(url, **self._set_request_timeout(kwargs))
File "/home/wdler/.local/lib/python3.6/site-packages/requests/sessions.py", line 555, in get
return self.request('GET', url, **kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/requests/sessions.py", line 542, in request
resp = self.send(prep, **send_kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/requests/sessions.py", line 655, in send
r = adapter.send(request, **kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/requests/adapters.py", line 498, in send
raise ConnectionError(err, request=request)
requests.exceptions.ConnectionError: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/wdler/miniwdl/WDL/runtime/task.py", line 164, in run_local_task
container = new_task_container(cfg, logger, run_id, run_dir)
File "/home/wdler/miniwdl/WDL/runtime/task_container.py", line 384, in new
backend_cls.global_init(cfg, logger)
File "/home/wdler/miniwdl/WDL/runtime/task_container.py", line 400, in global_init
client = docker.from_env(version="auto")
File "/home/wdler/.local/lib/python3.6/site-packages/docker/client.py", line 101, in from_env
**kwargs_from_env(**kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/docker/client.py", line 45, in __init__
self.api = APIClient(*args, **kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/docker/api/client.py", line 197, in __init__
self._version = self._retrieve_server_version()
File "/home/wdler/.local/lib/python3.6/site-packages/docker/api/client.py", line 222, in _retrieve_server_version
f'Error while fetching server API version: {e}'
docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/wdler/miniwdl/WDL/runtime/task.py", line 160, in run_local_task
cache,
File "/home/wdler/miniwdl/WDL/runtime/task.py", line 287, in _download_input_files
ans = Value.rewrite_env_paths(inputs, rewriter)
File "/home/wdler/miniwdl/WDL/Value.py", line 588, in rewrite_env_paths
return env.map(lambda binding: Env.Binding(binding.name, rewrite_paths(binding.value, f)))
File "/home/wdler/miniwdl/WDL/Env.py", line 151, in map
fb = f(b)
File "/home/wdler/miniwdl/WDL/Value.py", line 588, in <lambda>
return env.map(lambda binding: Env.Binding(binding.name, rewrite_paths(binding.value, f)))
File "/home/wdler/miniwdl/WDL/Value.py", line 578, in rewrite_paths
return map_paths(copy.deepcopy(v))
File "/home/wdler/miniwdl/WDL/Value.py", line 572, in map_paths
v2.value = f(v2)
File "/home/wdler/miniwdl/WDL/runtime/task.py", line 275, in rewriter
logger_prefix=logger_prefix + [f"download{downloads}"],
File "/home/wdler/miniwdl/WDL/runtime/download.py", line 148, in run_cached
filename = run(cfg, logger, uri, directory=directory, run_dir=run_dir, **kwargs)
File "/home/wdler/miniwdl/WDL/runtime/download.py", line 119, in run
raise DownloadFailed(uri) from exn.__cause__
WDL.runtime.error.DownloadFailed: unable to download https://google.com/robots.txt
2021-10-01 13:58:56.665 tests.test_4taskrun.TestTaskRunner.test_download_cache.t:lines ERROR task lines ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_miumshej/20211001_135856_lines", error: "DownloadFailed", message: "unable to download https://google.com/robots.txt"
2021-10-01 13:58:56.666 tests.test_4taskrun.TestTaskRunner.test_download_cache.t:lines.CallCache.FlockHolder DEBUG close :: file: "/tmp/miniwdl_test_taskrun_miumshej/20211001_135856_lines/task.log", exclusive: true
2021-10-01 13:58:56.571 tests.test_4taskrun.TestTaskRunner.test_download_cache.t:lines NOTICE task start :: name: "lines", source: "", line: 3, column: 9, dir: "/tmp/miniwdl_test_taskrun_miumshej/20211001_135856_lines", thread: 140007104997184
2021-10-01 13:58:56.572 tests.test_4taskrun.TestTaskRunner.test_download_cache.t:lines.CallCache.FlockHolder DEBUG flock :: file: "/tmp/miniwdl_test_taskrun_miumshej/20211001_135856_lines/task.log", realpath: "/tmp/miniwdl_test_taskrun_miumshej/20211001_135856_lines/task.log", exclusive: true, wait: false
2021-10-01 13:58:56.572 tests.test_4taskrun.TestTaskRunner.test_download_cache.t:lines.CallCache.FlockHolder DEBUG flocked :: file: "/tmp/miniwdl_test_taskrun_miumshej/20211001_135856_lines/task.log", realpath: "/tmp/miniwdl_test_taskrun_miumshej/20211001_135856_lines/task.log", exclusive: true, name_inode: 281, fd_inode: 281
2021-10-01 13:58:56.623 tests.test_4taskrun.TestTaskRunner.test_download_cache.t:lines INFO download input file :: uri: "https://google.com/robots.txt"
2021-10-01 13:58:56.624 tests.test_4taskrun.TestTaskRunner.test_download_cache.t:lines.CallCache DEBUG no download cache hit :: uri: "https://google.com/robots.txt", cache_path: "/tmp/miniwdl_test_taskrun_miumshej/cache/files/https/google.com/_/robots.txt"
2021-10-01 13:58:56.624 tests.test_4taskrun.TestTaskRunner.test_download_cache.t:lines INFO start download :: uri: "https://google.com/robots.txt"
2021-10-01 13:58:56.642 tests.test_4taskrun.TestTaskRunner.test_download_cache.t:lines.download0.t:download-aria2c NOTICE task start :: name: "aria2c", source: "", line: 2, column: 5, dir: "/tmp/miniwdl_test_taskrun_miumshej/cache/ops/20211001_135856_aria2c", thread: 140007104997184
2021-10-01 13:58:56.643 tests.test_4taskrun.TestTaskRunner.test_download_cache.t:lines.download0.t:download-aria2c.CallCache.FlockHolder DEBUG flock :: file: "/tmp/miniwdl_test_taskrun_miumshej/cache/ops/20211001_135856_aria2c/task.log", realpath: "/tmp/miniwdl_test_taskrun_miumshej/cache/ops/20211001_135856_aria2c/task.log", exclusive: true, wait: false
2021-10-01 13:58:56.644 tests.test_4taskrun.TestTaskRunner.test_download_cache.t:lines.download0.t:download-aria2c.CallCache.FlockHolder DEBUG flocked :: file: "/tmp/miniwdl_test_taskrun_miumshej/cache/ops/20211001_135856_aria2c/task.log", realpath: "/tmp/miniwdl_test_taskrun_miumshej/cache/ops/20211001_135856_aria2c/task.log", exclusive: true, name_inode: 294, fd_inode: 294
2021-10-01 13:58:56.663 tests.test_4taskrun.TestTaskRunner.test_download_cache.t:lines.download0.t:download-aria2c DEBUG Traceback (most recent call last):
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 706, in urlopen
chunked=chunked,
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 394, in _make_request
conn.request(method, url, **httplib_request_kw)
File "/usr/lib/python3.6/http/client.py", line 1281, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1327, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1276, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1042, in _send_output
self.send(msg)
File "/usr/lib/python3.6/http/client.py", line 980, in send
self.connect()
File "/home/wdler/.local/lib/python3.6/site-packages/docker/transport/unixconn.py", line 30, in connect
sock.connect(self.unix_socket)
FileNotFoundError: [Errno 2] No such file or directory
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/wdler/.local/lib/python3.6/site-packages/requests/adapters.py", line 449, in send
timeout=timeout
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 756, in urlopen
method, url, error=e, _pool=self, _stacktrace=sys.exc_info()[2]
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/util/retry.py", line 532, in increment
raise six.reraise(type(error), error, _stacktrace)
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/packages/six.py", line 769, in reraise
raise value.with_traceback(tb)
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 706, in urlopen
chunked=chunked,
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 394, in _make_request
conn.request(method, url, **httplib_request_kw)
File "/usr/lib/python3.6/http/client.py", line 1281, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1327, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1276, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1042, in _send_output
self.send(msg)
File "/usr/lib/python3.6/http/client.py", line 980, in send
self.connect()
File "/home/wdler/.local/lib/python3.6/site-packages/docker/transport/unixconn.py", line 30, in connect
sock.connect(self.unix_socket)
urllib3.exceptions.ProtocolError: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/wdler/.local/lib/python3.6/site-packages/docker/api/client.py", line 214, in _retrieve_server_version
return self.version(api_version=False)["ApiVersion"]
File "/home/wdler/.local/lib/python3.6/site-packages/docker/api/daemon.py", line 181, in version
return self._result(self._get(url), json=True)
File "/home/wdler/.local/lib/python3.6/site-packages/docker/utils/decorators.py", line 46, in inner
return f(self, *args, **kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/docker/api/client.py", line 237, in _get
return self.get(url, **self._set_request_timeout(kwargs))
File "/home/wdler/.local/lib/python3.6/site-packages/requests/sessions.py", line 555, in get
return self.request('GET', url, **kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/requests/sessions.py", line 542, in request
resp = self.send(prep, **send_kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/requests/sessions.py", line 655, in send
r = adapter.send(request, **kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/requests/adapters.py", line 498, in send
raise ConnectionError(err, request=request)
requests.exceptions.ConnectionError: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/wdler/miniwdl/WDL/runtime/task.py", line 164, in run_local_task
container = new_task_container(cfg, logger, run_id, run_dir)
File "/home/wdler/miniwdl/WDL/runtime/task_container.py", line 384, in new
backend_cls.global_init(cfg, logger)
File "/home/wdler/miniwdl/WDL/runtime/task_container.py", line 400, in global_init
client = docker.from_env(version="auto")
File "/home/wdler/.local/lib/python3.6/site-packages/docker/client.py", line 101, in from_env
**kwargs_from_env(**kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/docker/client.py", line 45, in __init__
self.api = APIClient(*args, **kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/docker/api/client.py", line 197, in __init__
self._version = self._retrieve_server_version()
File "/home/wdler/.local/lib/python3.6/site-packages/docker/api/client.py", line 222, in _retrieve_server_version
f'Error while fetching server API version: {e}'
docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))
2021-10-01 13:58:56.663 tests.test_4taskrun.TestTaskRunner.test_download_cache.t:lines.download0.t:download-aria2c ERROR task aria2c ( Ln 2 Col 5) failed :: dir: "/tmp/miniwdl_test_taskrun_miumshej/cache/ops/20211001_135856_aria2c", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:58:56.664 tests.test_4taskrun.TestTaskRunner.test_download_cache.t:lines.download0.t:download-aria2c.CallCache.FlockHolder DEBUG close :: file: "/tmp/miniwdl_test_taskrun_miumshej/cache/ops/20211001_135856_aria2c/task.log", exclusive: true
2021-10-01 13:58:56.665 tests.test_4taskrun.TestTaskRunner.test_download_cache.t:lines DEBUG Traceback (most recent call last):
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 706, in urlopen
chunked=chunked,
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 394, in _make_request
conn.request(method, url, **httplib_request_kw)
File "/usr/lib/python3.6/http/client.py", line 1281, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1327, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1276, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1042, in _send_output
self.send(msg)
File "/usr/lib/python3.6/http/client.py", line 980, in send
self.connect()
File "/home/wdler/.local/lib/python3.6/site-packages/docker/transport/unixconn.py", line 30, in connect
sock.connect(self.unix_socket)
FileNotFoundError: [Errno 2] No such file or directory
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/wdler/.local/lib/python3.6/site-packages/requests/adapters.py", line 449, in send
timeout=timeout
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 756, in urlopen
method, url, error=e, _pool=self, _stacktrace=sys.exc_info()[2]
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/util/retry.py", line 532, in increment
raise six.reraise(type(error), error, _stacktrace)
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/packages/six.py", line 769, in reraise
raise value.with_traceback(tb)
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 706, in urlopen
chunked=chunked,
File "/home/wdler/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 394, in _make_request
conn.request(method, url, **httplib_request_kw)
File "/usr/lib/python3.6/http/client.py", line 1281, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1327, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1276, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/usr/lib/python3.6/http/client.py", line 1042, in _send_output
self.send(msg)
File "/usr/lib/python3.6/http/client.py", line 980, in send
self.connect()
File "/home/wdler/.local/lib/python3.6/site-packages/docker/transport/unixconn.py", line 30, in connect
sock.connect(self.unix_socket)
urllib3.exceptions.ProtocolError: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/wdler/.local/lib/python3.6/site-packages/docker/api/client.py", line 214, in _retrieve_server_version
return self.version(api_version=False)["ApiVersion"]
File "/home/wdler/.local/lib/python3.6/site-packages/docker/api/daemon.py", line 181, in version
return self._result(self._get(url), json=True)
File "/home/wdler/.local/lib/python3.6/site-packages/docker/utils/decorators.py", line 46, in inner
return f(self, *args, **kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/docker/api/client.py", line 237, in _get
return self.get(url, **self._set_request_timeout(kwargs))
File "/home/wdler/.local/lib/python3.6/site-packages/requests/sessions.py", line 555, in get
return self.request('GET', url, **kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/requests/sessions.py", line 542, in request
resp = self.send(prep, **send_kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/requests/sessions.py", line 655, in send
r = adapter.send(request, **kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/requests/adapters.py", line 498, in send
raise ConnectionError(err, request=request)
requests.exceptions.ConnectionError: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/wdler/miniwdl/WDL/runtime/task.py", line 164, in run_local_task
container = new_task_container(cfg, logger, run_id, run_dir)
File "/home/wdler/miniwdl/WDL/runtime/task_container.py", line 384, in new
backend_cls.global_init(cfg, logger)
File "/home/wdler/miniwdl/WDL/runtime/task_container.py", line 400, in global_init
client = docker.from_env(version="auto")
File "/home/wdler/.local/lib/python3.6/site-packages/docker/client.py", line 101, in from_env
**kwargs_from_env(**kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/docker/client.py", line 45, in __init__
self.api = APIClient(*args, **kwargs)
File "/home/wdler/.local/lib/python3.6/site-packages/docker/api/client.py", line 197, in __init__
self._version = self._retrieve_server_version()
File "/home/wdler/.local/lib/python3.6/site-packages/docker/api/client.py", line 222, in _retrieve_server_version
f'Error while fetching server API version: {e}'
docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/wdler/miniwdl/WDL/runtime/task.py", line 160, in run_local_task
cache,
File "/home/wdler/miniwdl/WDL/runtime/task.py", line 287, in _download_input_files
ans = Value.rewrite_env_paths(inputs, rewriter)
File "/home/wdler/miniwdl/WDL/Value.py", line 588, in rewrite_env_paths
return env.map(lambda binding: Env.Binding(binding.name, rewrite_paths(binding.value, f)))
File "/home/wdler/miniwdl/WDL/Env.py", line 151, in map
fb = f(b)
File "/home/wdler/miniwdl/WDL/Value.py", line 588, in <lambda>
return env.map(lambda binding: Env.Binding(binding.name, rewrite_paths(binding.value, f)))
File "/home/wdler/miniwdl/WDL/Value.py", line 578, in rewrite_paths
return map_paths(copy.deepcopy(v))
File "/home/wdler/miniwdl/WDL/Value.py", line 572, in map_paths
v2.value = f(v2)
File "/home/wdler/miniwdl/WDL/runtime/task.py", line 275, in rewriter
logger_prefix=logger_prefix + [f"download{downloads}"],
File "/home/wdler/miniwdl/WDL/runtime/download.py", line 148, in run_cached
filename = run(cfg, logger, uri, directory=directory, run_dir=run_dir, **kwargs)
File "/home/wdler/miniwdl/WDL/runtime/download.py", line 119, in run
raise DownloadFailed(uri) from exn.__cause__
WDL.runtime.error.DownloadFailed: unable to download https://google.com/robots.txt
2021-10-01 13:58:56.665 tests.test_4taskrun.TestTaskRunner.test_download_cache.t:lines ERROR task lines ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_miumshej/20211001_135856_lines", error: "DownloadFailed", message: "unable to download https://google.com/robots.txt"
2021-10-01 13:58:56.666 tests.test_4taskrun.TestTaskRunner.test_download_cache.t:lines.CallCache.FlockHolder DEBUG close :: file: "/tmp/miniwdl_test_taskrun_miumshej/20211001_135856_lines/task.log", exclusive: true
2021-10-01 13:58:57.274 tests.test_4taskrun.TestTaskRunner.test_download_input_files.t:lines.download0.t:download-aria2c ERROR task aria2c ( Ln 2 Col 5) failed :: dir: "/tmp/miniwdl_test_taskrun_naw95k3c/20211001_135857_lines/download/0", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:58:57.275 tests.test_4taskrun.TestTaskRunner.test_download_input_files.t:lines ERROR task lines ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_naw95k3c/20211001_135857_lines", error: "DownloadFailed", message: "unable to download https://google.com/robots.txt"
2021-10-01 13:58:57.274 tests.test_4taskrun.TestTaskRunner.test_download_input_files.t:lines.download0.t:download-aria2c ERROR task aria2c ( Ln 2 Col 5) failed :: dir: "/tmp/miniwdl_test_taskrun_naw95k3c/20211001_135857_lines/download/0", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:58:57.275 tests.test_4taskrun.TestTaskRunner.test_download_input_files.t:lines ERROR task lines ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_naw95k3c/20211001_135857_lines", error: "DownloadFailed", message: "unable to download https://google.com/robots.txt"
2021-10-01 13:59:00.496 tests.test_4taskrun.TestTaskRunner.test_optional_file_outputs.t:rmdir ERROR task rmdir ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_ogswkgam/20211001_135900_rmdir", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:59:00.496 tests.test_4taskrun.TestTaskRunner.test_optional_file_outputs.t:rmdir ERROR task rmdir ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_ogswkgam/20211001_135900_rmdir", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:58:59.020 tests.test_4taskrun.TestTaskRunner.test_hello_file.t:hello_file ERROR task hello_file ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_q6nmk9su/20211001_135858_hello_file", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:58:59.020 tests.test_4taskrun.TestTaskRunner.test_hello_file.t:hello_file ERROR task hello_file ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_q6nmk9su/20211001_135858_hello_file", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:58:58.721 tests.test_4taskrun.TestTaskRunner.test_hello_blank.t:hello_blank ERROR task hello_blank ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_qzfpak9j/20211001_135858_hello_blank", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:58:58.721 tests.test_4taskrun.TestTaskRunner.test_hello_blank.t:hello_blank ERROR task hello_blank ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_qzfpak9j/20211001_135858_hello_blank", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:58:56.079 tests.test_4taskrun.TestTaskRunner.test_delete_work.t:xxx ERROR task xxx ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_spl384fy/20211001_135856_xxx", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:58:56.079 tests.test_4taskrun.TestTaskRunner.test_delete_work.t:xxx ERROR task xxx ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_spl384fy/20211001_135856_xxx", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:59:02.367 tests.test_4taskrun.TestTaskRunner.test_signal.t:t ERROR task t ( Ln 3 Col 13) failed :: dir: "/tmp/miniwdl_test_taskrun_u88gd8or/20211001_135902_t", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:59:02.367 tests.test_4taskrun.TestTaskRunner.test_signal.t:t ERROR task t ( Ln 3 Col 13) failed :: dir: "/tmp/miniwdl_test_taskrun_u88gd8or/20211001_135902_t", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:58:55.444 tests.test_4taskrun.TestTaskRunner.test_compound_files.t:hello ERROR task hello ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_voxp4mg7/20211001_135855_hello", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:58:55.444 tests.test_4taskrun.TestTaskRunner.test_compound_files.t:hello ERROR task hello ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_voxp4mg7/20211001_135855_hello", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:59:02.929 tests.test_4taskrun.TestTaskRunner.test_weird_output_files.t:hello ERROR task hello ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_vrqphf9l/20211001_135902_hello", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:59:02.929 tests.test_4taskrun.TestTaskRunner.test_weird_output_files.t:hello ERROR task hello ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_vrqphf9l/20211001_135902_hello", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:59:01.250 tests.test_4taskrun.TestTaskRunner.test_plugins.t:inc.my_plugin CRITICAL hello
2021-10-01 13:59:01.253 tests.test_4taskrun.TestTaskRunner.test_plugins.t:inc.my_plugin CRITICAL goodbye
2021-10-01 13:59:01.254 tests.test_4taskrun.TestTaskRunner.test_plugins.t:inc ERROR task inc ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_xabhd7zu/20211001_135901_inc", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:59:01.250 tests.test_4taskrun.TestTaskRunner.test_plugins.t:inc.my_plugin CRITICAL hello
2021-10-01 13:59:01.253 tests.test_4taskrun.TestTaskRunner.test_plugins.t:inc.my_plugin CRITICAL goodbye
2021-10-01 13:59:01.254 tests.test_4taskrun.TestTaskRunner.test_plugins.t:inc ERROR task inc ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_xabhd7zu/20211001_135901_inc", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:58:54.368 tests.test_4taskrun.TestTaskRunner.test_command_escaping.t:hello ERROR task hello ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_xgkdec3c/20211001_135854_hello", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:58:54.368 tests.test_4taskrun.TestTaskRunner.test_command_escaping.t:hello ERROR task hello ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_xgkdec3c/20211001_135854_hello", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:59:02.792 tests.test_4taskrun.TestTaskRunner.test_topsort.t:t ERROR task t ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_zeimu181/20211001_135902_t", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
2021-10-01 13:59:02.792 tests.test_4taskrun.TestTaskRunner.test_topsort.t:t ERROR task t ( Ln 3 Col 9) failed :: dir: "/tmp/miniwdl_test_taskrun_zeimu181/20211001_135902_t", error: "DockerException", message: "Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))"
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment