Intermittent workflow errors with local galaxy running postgresql 9.3 - galaxy-dev

4 Oct 2013


      Hi All,
We have been having issues with workflows generating intermittent errors using sqlite. We recently converted to postgresql  9.3 in an attempt to resolve the issue as suggested in prior posts. Despite switching to postgresql we continue to have these errors. Does anyone have any additional suggestions that may resolve this issue?
Thanks,
Todd
Traceback (most recent call last):
  File "/opt/paml/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 122, in prepare_job
    job_wrapper.runner_command_line = self.build_command_line( job_wrapper, include_metadata=include_metadata, include_work_dir_outputs=include_work_dir_outputs )
  File "/opt/paml/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 172, in build_command_line
    work_dir_outputs = self.get_work_dir_outputs( job_wrapper )
  File "/opt/paml/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 222, in get_work_dir_outputs
    for dataset in dataset_assoc.dataset.dataset.history_associations + dataset_assoc.dataset.dataset.library_associations:
  File "/opt/paml/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/attributes.py", line 168, in __get__
    return self.impl.get(instance_state(instance),dict_)
  File "/opt/paml/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/attributes.py", line 453, in get
    value = self.callable_(state, passive)
  File "/opt/paml/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/strategies.py", line 508, in _load_for_state
    return self._emit_lazyload(session, state, ident_key)
  File "/opt/paml/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/strategies.py", line 574, in _emit_lazyload
    result = q.all()
  File "/opt/paml/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py", line 2115, in all
    return list(self)
  File "/opt/paml/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py", line 2227, in __iter__
    return self._execute_and_instances(context)
  File "/opt/paml/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py", line 2242, in _execute_and_instances
    result = conn.execute(querycontext.statement, self._params)
  File "/opt/paml/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1449, in execute
    params)
  File "/opt/paml/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 "/opt/paml/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 "/opt/paml/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 "/opt/paml/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)
OperationalError: (OperationalError) database is locked u'SELECT library_dataset_dataset_association.id AS library_dataset_dataset_association_id,
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