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
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