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 > [email protected] > http://lists.bx.psu.edu/listinfo/galaxy-dev _______________________________________________ galaxy-dev mailing list [email protected] http://lists.bx.psu.edu/listinfo/galaxy-dev
