One per second? Can you tell me more about your configuration? This is an odd bug with multiple mapper initialization that I haven't been able to reproduce yet, so any information will help. Database configuration, number of processes, etc. On Oct 7, 2014 11:46 AM, "Ulf Schaefer" Ulf.Schaefer@phe.gov.uk wrote:
Dear all
Maybe one of you can shed some light on this error message that I see in the log file for one of my handler processes. I get about one of them per second. The effect is that most of the jobs remain in the "waiting to run" stage.
The postgres database is running on a separate server and appear to be doing just fine.
Any help is greatly appreciated.
Thanks Ulf
galaxy.jobs.handler ERROR 2014-10-07 10:32:24,676 Exception in monitor_step Traceback (most recent call last): File
"/phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/lib/galaxy/jobs/handler.py", line 161, in __monitor self.__monitor_step() File
"/phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/lib/galaxy/jobs/handler.py", line 184, in __monitor_step hda_not_ready = self.sa_session.query(model.Job.id).enable_eagerloads(False) \ File
"/phengs/hpc_storage/home/galaxy_hpc/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
"/phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1088, in query return self._query_cls(entities, self, **kwargs) File
"/phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py", line 108, in __init__ self._set_entities(entities) File
"/phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py", line 117, in _set_entities self._setup_aliasizers(self._entities) File
"/phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py", line 132, in _setup_aliasizers _entity_info(entity) File
"/phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/util.py", line 578, in _entity_info mapperlib.configure_mappers() File
"/phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py", line 2260, in configure_mappers raise e InvalidRequestError: One or more mappers failed to initialize - can't proceed with initialization of other mappers. Original exception was: When initializing mapper Mapper|Queue|kombu_queue, expression 'Message' failed to locate a name ("name 'Message' is not defined"). If this is a class name, consider adding this relationship() to the <class 'kombu.transport.sqlalchemy.Queue'> class after both dependent classes have been defined.
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