New subject: MySQL server has gone away error: solved

21 Jan 2011


      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.
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]
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