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.schae...@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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