Hey,
I wanted to know if anyone else has had experience with database deadlock
when using dataset collections and running a large number of samples
through a workflow.
Traceback (most recent call last):
File
"/Warehouse/Applications/irida/galaxy/galaxy-dist/lib/galaxy/jobs/runners/__init__.py",
line 565, in finish_job
job_state.job_wrapper.finish( stdout, stderr, exit_code )
File
"/Warehouse/Applications/irida/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py",
line 1250, in finish
self.sa_session.flush()
File
"/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py",
line 114, in do
return getattr(self.registry(), name)(*args, **kwargs)
File
"/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py",
line 1718, in flush
self._flush(objects)
File
"/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py",
line 1789, in _flush
flush_context.execute()
File
"/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.py",
line 331, in execute
rec.execute(self)
File
"/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.py",
line 475, in execute
uow
File
"/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py",
line 59, in save_obj
mapper, table, update)
File
"/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py",
line 485, in _emit_update_statements
execute(statement, params)
File
"/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
line 1449, in execute
params)
File
"/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
line 1584, in _execute_clauseelement
compiled_sql, distilled_params
File
"/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
line 1698, in _execute_context
context)
File
"/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
line 1691, in _execute_context
context)
File
"/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py",
line 331, in do_execute
cursor.execute(statement, parameters)
DBAPIError: (TransactionRollbackError) deadlock detected
DETAIL: Process 25859 waits for ShareLock on transaction 144373;
blocked by process 25858.
Process 25858 waits for ShareLock on transaction 144372; blocked by
process 25859.
HINT: See server log for query details.
'UPDATE workflow_invocation SET update_time=%(update_time)s WHERE
workflow_invocation.id = %(workflow_invocation_id)s' {'update_time':
datetime.datetime(2015, 2, 27, 3, 51, 57, 81403),
'workflow_invocation_id': 48}
I saw this post
http://dev.list.galaxyproject.org/data-collections-workflow-bug-td4666496.html
with a similar issue and the solution was to make sure not to use a
sqlite database, but I'm using a postgres database and still
encountered this issue. This was after running a very large number of
samples (~200) using dataset collections. Just wondering if anyone
else was running into this issue?
Thanks,
Aaron
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
