Hi Dannon
I am running 6 handler and 6 web processes. I have the latest stable
version of the code (from June 2nd 2014). My postgres database (version
8.4.9) is running on a different server on the same subnet. Both servers
are Centos (6.5 on the Galaxy server, 6.2 on the database server). Jobs
are supposed to be dispatched to a dedicated queue on a cluster running
Univa Grid Engine. But I don't think the jobs get dispatched to the
cluster because of a previous database communication problem.
The reason that I have so many error messages might be that there were
quite a number of jobs waiting to run.
Please let me know if you want to know anything more specific. I'd be
happy to send any configuration files.
Thanks for your help.
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.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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