Marina Gourtovaia wrote:
> Hello
> 
> My Galaxy instance suffers from 'MySQL server has gone away error'.
> This error appears if the last web request was more than ~30-60 sec
> ago.  The full traceback follows at the end of this message. If the
> same request is resent, everything is OK. My universe_wsgi.ini
> config file is set up as recommended for mysql. All timeouts on the
> database server itself are set well above 1min.

Hi Marina,

What value do you have set for 'database_engine_option_pool_recycle' in
universe_wsgi.ini?  Have you tried smaller values?

--nate

> 
> This occurs both on etch and lenny Linux 64 bit nodes. The python
> version is 2.4
> 
> I would be helpful for any suggestions. Can move to postgresql, but
> rather stay with mysql.
> 
> Marina Gourtovaia
> 
> URL: http://sf-2-1-02.internal.sanger.ac.uk:9700/
> File 
> '/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/eggs/Paste-1.6-py2.4.egg/paste/exceptions/errormiddleware.py',
> line 143 in __call__
>   app_iter = self.application(environ, start_response)
> File 
> '/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/eggs/Paste-1.6-py2.4.egg/paste/debug/prints.py',
> line 97 in __call__
>   status, headers, body = wsgilib.intercept_output(
> File 
> '/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/eggs/Paste-1.6-py2.4.egg/paste/wsgilib.py',
> line 539 in intercept_output
>   app_iter = application(environ, replacement_start_response)
> File 
> '/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/eggs/Paste-1.6-py2.4.egg/paste/recursive.py',
> line 80 in __call__
>   return self.application(environ, start_response)
> File 
> '/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/eggs/Paste-1.6-py2.4.egg/paste/httpexceptions.py',
> line 632 in __call__
>   return self.application(environ, start_response)
> File 
> '/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/lib/galaxy/web/framework/base.py',
> line 119 in __call__
>   trans = self.transaction_factory( environ )
> File 
> '/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py',
> line 161 in <lambda>
>   self.set_transaction_factory( lambda e: self.transaction_chooser(
> e, galaxy_app, session_cookie ) )
> File 
> '/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py',
> line 181 in transaction_chooser
>   return GalaxyWebUITransaction( environ, galaxy_app, self,
> session_cookie )
> File 
> '/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py',
> line 791 in __init__
>   self._ensure_valid_session( session_cookie )
> File 
> '/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py',
> line 318 in _ensure_valid_session
>   self.app.model.GalaxySession.table.c.is_valid==True ) ) \
> File 
> '/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/query.py',
> line 1300 in first
>   ret = list(self[0:1])
> File 
> '/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/query.py',
> line 1221 in __getitem__
>   return list(res)
> File 
> '/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/query.py',
> line 1361 in __iter__
>   return self._execute_and_instances(context)
> File 
> '/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/query.py',
> line 1364 in _execute_and_instances
>   result = self.session.execute(querycontext.statement,
> params=self._params, mapper=self._mapper_zero_or_none())
> File 
> '/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/session.py',
> line 754 in execute
>   return self.__connection(engine, close_with_result=True).execute(
> File 
> '/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/base.py',
> line 824 in execute
>   return Connection.executors[c](self, object, multiparams, params)
> File 
> '/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/base.py',
> line 874 in _execute_clauseelement
>   return self.__execute_context(context)
> File 
> '/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/base.py',
> line 896 in __execute_context
>   self._cursor_execute(context.cursor, context.statement,
> context.parameters[0], context=context)
> File 
> '/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/base.py',
> line 950 in _cursor_execute
>   self._handle_dbapi_exception(e, statement, parameters, cursor, context)
> File 
> '/nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/base.py',
> line 931 in _handle_dbapi_exception
>   raise exc.DBAPIError.instance(statement, parameters, e,
> connection_invalidated=is_disconnect)
> OperationalError: (OperationalError) (2006, 'MySQL server has gone
> away') u'SELECT galaxy_session.id AS galaxy_session_id,
> galaxy_session.create_time AS galaxy_session_create_time,
> galaxy_session.update_time AS galaxy_session_update_time,
> galaxy_session.user_id AS galaxy_session_user_id,
> galaxy_session.remote_host AS galaxy_session_remote_host,
> galaxy_session.remote_addr AS galaxy_session_remote_addr,
> galaxy_session.referer AS galaxy_session_referer,
> galaxy_session.current_history_id AS
> galaxy_session_current_history_id, galaxy_session.session_key AS
> galaxy_session_session_key, galaxy_session.is_valid AS
> galaxy_session_is_valid, galaxy_session.prev_session_id AS
> galaxy_session_prev_session_id \nFROM galaxy_session \nWHERE
> galaxy_session.session_key = %s AND galaxy_session.is_valid = %s \n
> LIMIT 0, 1' ['6683a26145119b72ce04fc6d4c6d7a0f', 1]
> 
> 
> -- 
> The Wellcome Trust Sanger Institute is operated by Genome Research
> Limited, a charity registered in England with number 1021457 and a
> company registered in England with number 2742969, whose registered
> office is 215 Euston Road, London, NW1 2BE.
> _______________________________________________
> galaxy-dev mailing list
> galaxy-dev@lists.bx.psu.edu
> http://lists.bx.psu.edu/listinfo/galaxy-dev
_______________________________________________
galaxy-dev mailing list
galaxy-dev@lists.bx.psu.edu
http://lists.bx.psu.edu/listinfo/galaxy-dev

Reply via email to