Update: The usual switching it off and on again (server reboot) has resolved the problem (for now), albeit in a rather unsatisfactory manner. If there are any insights what caused this behaviour and how it can be avoided in the future I'd be more than happy to hear them. Cheers Ulf On 07/10/14 11:04, Dannon Baker wrote:
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
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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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