Hi Folks,
So I managed to ran through the ansible. What I did was to remove certain
steps. For example, I don't need slurm-drmaa and docker, then I skipped the
update cache. After these minor changes, it finished successfully(?) with
an error message it ignored. Then I tried to access the UI, but nothing
worked. I pasted it below for your reference. If anyone has seen this
before, please help. :-)
Sorry for the beginner question, so once the ansible playbook ran
through...seems the galaxy and the postgresql etc were started. How do I
start/stop them manually? Do I have to run the playbook every time I want
to run galaxy or only after I modify the playbook? Also, if I don't look at
the log, I don't even know that the UI is at 127.0.0.1:4001. Is there any
documentation for this?
Thanks,
Rui
error message:
galaxy.web.stack INFO 2018-10-12 19:41:53,874 [p:102477,w:1,m:0]
[MainThread] Galaxy server instance 'main.web.1' is running
Starting server in PID 101567.
serving on uwsgi://127.0.0.1:4001
galaxy.jobs.handler ERROR 2018-10-12 19:42:48,487 [p:102477,w:1,m:0]
[JobHandlerQueue.monitor_thread] Exception in monitor_step
Traceback (most recent call last):
File "lib/galaxy/jobs/handler.py", line 213, in __monitor
self.__monitor_step()
File "lib/galaxy/jobs/handler.py", line 272, in __monitor_step
.order_by(model.Job.id).all()
File
"/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py",
line 2737, in all
return list(self)
File
"/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py",
line 2889, in __iter__
return self._execute_and_instances(context)
File
"/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py",
line 2912, in _execute_and_instances
result = conn.execute(querycontext.statement, self._params)
File
"/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py",
line 948, in execute
return meth(self, multiparams, params)
File
"/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/sql/elements.py",
line 269, in _execute_on_connection
return connection._execute_clauseelement(self, multiparams, params)
File
"/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py",
line 1060, in _execute_clauseelement
compiled_sql, distilled_params
File
"/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py",
line 1200, in _execute_context
context)
File
"/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py",
line 1413, in _handle_dbapi_exception
exc_info
File
"/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/compat.py",
line 203, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb, cause=cause)
File
"/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py",
line 1193, in _execute_context
context)
File
"/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py",
line 507, in do_execute
cursor.execute(statement, parameters)
OperationalError: (psycopg2.OperationalError) server closed the connection
unexpectedly
This probably means the server terminated abnormally
before or while processing the request.
[SQL: 'SELECT EXISTS (SELECT history_dataset_association.id,
history_dataset_association.history_id,
history_dataset_association.dataset_id,
history_dataset_association.create_time,
history_dataset_association.update_time, history_dataset_association.state,
history_dataset_association.copied_from_history_dataset_association_id,
history_dataset_association.copied_from_library_dataset_dataset_association_id,
history_dataset_association.name, history_dataset_association.info,
history_dataset_association.blurb, history_dataset_association.peek,
history_dataset_association.tool_version,
history_dataset_association.extension,
history_dataset_association.metadata,
history_dataset_association.parent_id,
history_dataset_association.designation,
history_dataset_association.deleted, history_dataset_association.visible,
history_dataset_association.extended_metadata_id,
history_dataset_association.version, history_dataset_association.hid,
history_dataset_association.purged,
history_dataset_association.hidden_beneath_collection_instance_id \nFROM
history_dataset_association, job_to_output_dataset \nWHERE job.id =
job_to_output_dataset.job_id AND history_dataset_association.id =
job_to_output_dataset.dataset_id AND history_dataset_association.deleted =
true) AS anon_1, EXISTS (SELECT history_dataset_collection_association.id
\nFROM history_dataset_collection_association,
job_to_output_dataset_collection \nWHERE job.id =
job_to_output_dataset_collection.job_id AND
history_dataset_collection_association.id =
job_to_output_dataset_collection.dataset_collection_id AND
history_dataset_collection_association.deleted = true) AS anon_2, job.id AS
job_id, job.create_time AS job_create_time, job.update_time AS
job_update_time, job.history_id AS job_history_id, job.library_folder_id AS
job_library_folder_id, job.tool_id AS job_tool_id, job.tool_version AS
job_tool_version, job.state AS job_state, job.info AS job_info,
job.copied_from_job_id AS job_copied_from_job_id, job.command_line AS
job_command_line, job.dependencies AS job_dependencies, job.param_filename
AS job_param_filename, job.runner_name AS job_runner_name_1, job.stdout AS
job_stdout, job.stderr AS job_stderr, job.exit_code AS job_exit_code,
job.traceback AS job_traceback, job.session_id AS job_session_id,
job.user_id AS job_user_id, job.job_runner_name AS job_job_runner_name,
job.job_runner_external_id AS job_job_runner_external_id,
job.destination_id AS job_destination_id, job.destination_params AS
job_destination_params, job.object_store_id AS job_object_store_id,
job.imported AS job_imported, job.params AS job_params, job.handler AS
job_handler \nFROM job \nWHERE job.state = %(state_1)s AND job.handler =
%(handler_1)s AND job.id NOT IN (SELECT job.id \nFROM job JOIN
job_to_input_dataset ON job.id = job_to_input_dataset.job_id JOIN
history_dataset_association ON history_dataset_association.id =
job_to_input_dataset.dataset_id JOIN dataset ON dataset.id =
history_dataset_association.dataset_id \nWHERE job.state = %(state_2)s AND
(history_dataset_association.state = %(_state_1)s OR
history_dataset_association.deleted = true OR dataset.state != %(state_3)s
OR dataset.deleted = true)) AND job.id NOT IN (SELECT job.id \nFROM job
JOIN job_to_input_library_dataset ON job.id =
job_to_input_library_dataset.job_id JOIN
library_dataset_dataset_association ON
library_dataset_dataset_association.id =
job_to_input_library_dataset.ldda_id JOIN dataset ON dataset.id =
library_dataset_dataset_association.dataset_id \nWHERE job.state =
%(state_4)s AND (library_dataset_dataset_association.state IS NOT NULL OR
library_dataset_dataset_association.deleted = true OR dataset.state !=
%(state_5)s OR dataset.deleted = true)) ORDER BY job.id'] [parameters:
{'state_3': 'ok', 'handler_1': 'main.web.1', 'state_1': 'new', '_state_1':
'failed_metadata', 'state_2': 'new', 'state_5': 'ok', 'state_4': 'new'}]
(Background on this error at: http://sqlalche.me/e/e3q8)
galaxy.jobs.handler ERROR 2018-10-12 19:42:48,488 [p:102478,w:2,m:0]
[JobHandlerQueue.monitor_thread] Exception in monitor_step
Traceback (most recent call last):
File "lib/galaxy/jobs/handler.py", line 213, in __monitor
self.__monitor_step()
File "lib/galaxy/jobs/handler.py", line 272, in __monitor_step
.order_by(model.Job.id).all()
File
"/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py",
line 2737, in all
return list(self)
File
"/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py",
line 2889, in __iter__
return self._execute_and_instances(context)
File
"/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py",
line 2912, in _execute_and_instances
result = conn.execute(querycontext.statement, self._params)
File
"/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py",
line 948, in execute
return meth(self, multiparams, params)
File
"/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/sql/elements.py",
line 269, in _execute_on_connection
return connection._execute_clauseelement(self, multiparams, params)
File
"/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py",
line 1060, in _execute_clauseelement
compiled_sql, distilled_params
File
"/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py",
line 1200, in _execute_context
context)
File
"/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py",
line 1413, in _handle_dbapi_exception
exc_info
File
"/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/compat.py",
line 203, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb, cause=cause)
File
"/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py",
line 1193, in _execute_context
context)
File
"/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py",
line 507, in do_execute
cursor.execute(statement, parameters)
OperationalError: (psycopg2.OperationalError) server closed the connection
unexpectedly
This probably means the server terminated abnormally
before or while processing the request.
[SQL: 'SELECT EXISTS (SELECT history_dataset_association.id,
history_dataset_association.history_id,
history_dataset_association.dataset_id,
history_dataset_association.create_time,
history_dataset_association.update_time, history_dataset_association.state,
history_dataset_association.copied_from_history_dataset_association_id,
history_dataset_association.copied_from_library_dataset_dataset_association_id,
history_dataset_association.name, history_dataset_association.info,
history_dataset_association.blurb, history_dataset_association.peek,
history_dataset_association.tool_version,
history_dataset_association.extension,
history_dataset_association.metadata,
history_dataset_association.parent_id,
history_dataset_association.designation,
history_dataset_association.deleted, history_dataset_association.visible,
history_dataset_association.extended_metadata_id,
history_dataset_association.version, history_dataset_association.hid,
history_dataset_association.purged,
history_dataset_association.hidden_beneath_collection_instance_id \nFROM
history_dataset_association, job_to_output_dataset \nWHERE job.id =
job_to_output_dataset.job_id AND history_dataset_association.id =
job_to_output_dataset.dataset_id AND history_dataset_association.deleted =
true) AS anon_1, EXISTS (SELECT history_dataset_collection_association.id
\nFROM history_dataset_collection_association,
job_to_output_dataset_collection \nWHERE job.id =
job_to_output_dataset_collection.job_id AND
history_dataset_collection_association.id =
job_to_output_dataset_collection.dataset_collection_id AND
history_dataset_collection_association.deleted = true) AS anon_2, job.id AS
job_id, job.create_time AS job_create_time, job.update_time AS
job_update_time, job.history_id AS job_history_id, job.library_folder_id AS
job_library_folder_id, job.tool_id AS job_tool_id, job.tool_version AS
job_tool_version, job.state AS job_state, job.info AS job_info,
job.copied_from_job_id AS job_copied_from_job_id, job.command_line AS
job_command_line, job.dependencies AS job_dependencies, job.param_filename
AS job_param_filename, job.runner_name AS job_runner_name_1, job.stdout AS
job_stdout, job.stderr AS job_stderr, job.exit_code AS job_exit_code,
job.traceback AS job_traceback, job.session_id AS job_session_id,
job.user_id AS job_user_id, job.job_runner_name AS job_job_runner_name,
job.job_runner_external_id AS job_job_runner_external_id,
job.destination_id AS job_destination_id, job.destination_params AS
job_destination_params, job.object_store_id AS job_object_store_id,
job.imported AS job_imported, job.params AS job_params, job.handler AS
job_handler \nFROM job \nWHERE job.state = %(state_1)s AND job.handler =
%(handler_1)s AND job.id NOT IN (SELECT job.id \nFROM job JOIN
job_to_input_dataset ON job.id = job_to_input_dataset.job_id JOIN
history_dataset_association ON history_dataset_association.id =
job_to_input_dataset.dataset_id JOIN dataset ON dataset.id =
history_dataset_association.dataset_id \nWHERE job.state = %(state_2)s AND
(history_dataset_association.state = %(_state_1)s OR
history_dataset_association.deleted = true OR dataset.state != %(state_3)s
OR dataset.deleted = true)) AND job.id NOT IN (SELECT job.id \nFROM job
JOIN job_to_input_library_dataset ON job.id =
job_to_input_library_dataset.job_id JOIN
library_dataset_dataset_association ON
library_dataset_dataset_association.id =
job_to_input_library_dataset.ldda_id JOIN dataset ON dataset.id =
library_dataset_dataset_association.dataset_id \nWHERE job.state =
%(state_4)s AND (library_dataset_dataset_association.state IS NOT NULL OR
library_dataset_dataset_association.deleted = true OR dataset.state !=
%(state_5)s OR dataset.deleted = true)) ORDER BY job.id'] [parameters:
{'state_3': 'ok', 'handler_1': 'main.web.2', 'state_1': 'new', '_state_1':
'failed_metadata', 'state_2': 'new', 'state_5': 'ok', 'state_4': 'new'}]
(Background on this error at: http://sqlalche.me/e/e3q8)
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