MySQL server has gone away error
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] -- 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.
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
Hi Nate It's set to 7200. Changing it to 200 or even to -1(!) does not make any difference. Marina On 21/01/2011 15:31, Nate Coraor wrote:
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
-- 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.
Hi The documentation for _mysql.c for function _mysql_ConnectionObject_ping states that this method assepts an optional parameter. If True, the client will attempt to reconnect. By default this is true in MyQSL<5.0.3 and off thereafter. My version of MySQL is 5.0.51a. Could this be a problem? Marina On 21/01/2011 15:45, Marina Gourtovaia wrote:
Hi Nate
It's set to 7200. Changing it to 200 or even to -1(!) does not make any difference.
Marina
On 21/01/2011 15:31, Nate Coraor wrote:
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
-- 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.
Hi Marina we are using 5.0.51a without any problem. Regards, Hans On 01/24/2011 04:20 PM, Marina Gourtovaia wrote:
Hi
The documentation for _mysql.c for function _mysql_ConnectionObject_ping states that this method assepts an optional parameter. If True, the client will attempt to reconnect. By default this is true in MyQSL<5.0.3 and off thereafter. My version of MySQL is 5.0.51a. Could this be a problem?
Marina
On 21/01/2011 15:45, Marina Gourtovaia wrote:
Hi Nate
It's set to 7200. Changing it to 200 or even to -1(!) does not make any difference.
Marina
On 21/01/2011 15:31, Nate Coraor wrote:
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
Hi Hans Thanks, good to know. Not sure how to nail this problem... Marina On 24/01/2011 16:02, Hans-Rudolf Hotz wrote:
Hi Marina
we are using 5.0.51a without any problem.
Regards, Hans
On 01/24/2011 04:20 PM, Marina Gourtovaia wrote:
Hi
The documentation for _mysql.c for function _mysql_ConnectionObject_ping states that this method assepts an optional parameter. If True, the client will attempt to reconnect. By default this is true in MyQSL<5.0.3 and off thereafter. My version of MySQL is 5.0.51a. Could this be a problem?
Marina
On 21/01/2011 15:45, Marina Gourtovaia wrote:
Hi Nate
It's set to 7200. Changing it to 200 or even to -1(!) does not make any difference.
Marina
On 21/01/2011 15:31, Nate Coraor wrote:
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
-- 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.
Hello My saga continues Here is what happens to teh pool of connections 2011-01-25 16:26:42,549 INFO sqlalchemy.engine.threadlocal.TLEngine.0x...49d0 ['b48ba2c1265b649d9dd83d1a0c2c2936', 1] sqlalchemy.engine.threadlocal.TLEngine.0x...49d0 INFO 2011-01-25 16:26:42,549 ['b48ba2c1265b649d9dd83d1a0c2c2936', 1] 2011-01-25 16:26:42,550 INFO sqlalchemy.pool.QueuePool.0x...eed0 Invalidate connection <_mysql.connection open to 'mcs3a' at 50c38c0> (reason: OperationalError:(2006, 'MySQL server has gone away')) sqlalchemy.pool.QueuePool.0x...eed0 INFO 2011-01-25 16:26:42,550 Invalidate connection <_mysql.connection open to 'mcs3a' at 50c38c0> (reason: OperationalError:(2006, 'MySQL server has gone away')) 2011-01-25 16:26:42,550 INFO sqlalchemy.pool.QueuePool.0x...eed0 Closing connection <_mysql.connection open to 'mcs3a' at 50c38c0> sqlalchemy.pool.QueuePool.0x...eed0 INFO 2011-01-25 16:26:42,550 Closing connection <_mysql.connection open to 'mcs3a' at 50c38c0> 2011-01-25 16:26:42,550 INFO sqlalchemy.pool.QueuePool.0x...eed0 Connection None being returned to pool sqlalchemy.pool.QueuePool.0x...eed0 INFO 2011-01-25 16:26:42,550 Connection None being returned to pool 2011-01-25 16:26:42,550 INFO sqlalchemy.pool.QueuePool.0x...eed0 Closing connection <_mysql.connection open to 'mcs3a' at 51343e0> sqlalchemy.pool.QueuePool.0x...eed0 INFO 2011-01-25 16:26:42,550 Closing connection <_mysql.connection open to 'mcs3a' at 51343e0> 2011-01-25 16:26:42,551 INFO sqlalchemy.pool.QueuePool.0x...eed0 Pool disposed. Pool size: 5 Connections in pool: 0 Current Overflow: -5 Current Checked out connections: 0 sqlalchemy.pool.QueuePool.0x...eed0 INFO 2011-01-25 16:26:42,551 Pool disposed. Pool size: 5 Connections in pool: 0 Current Overflow: -5 Current Checked out connections: 0 2011-01-25 16:26:42,551 INFO sqlalchemy.pool.QueuePool.0x...eed0 Pool recreating sqlalchemy.pool.QueuePool.0x...eed0 INFO 2011-01-25 16:26:42,551 Pool recreating 172.19.31.115 - - [25/Jan/2011:16:26:42 +0100] "GET /tool_runner?tool_id=addValue HTTP/1.1" 500 - "http://sf-5-1-01.internal.sanger.ac.uk:9700/root/tool_menu" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en; rv:1.9.0.19) Gecko/2010111021 Camino/2.0.6 (like Firefox/3.0.19)" Error - <class 'sqlalchemy.exc.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' ['b48ba2c1265b649d9dd83d1a0c2c2936', 1] Why doesn't Galaxy initiate a new pool in this situation? Marina On 24/01/2011 16:09, Marina Gourtovaia wrote:
Hi Hans
Thanks, good to know. Not sure how to nail this problem...
Marina
On 24/01/2011 16:02, Hans-Rudolf Hotz wrote:
Hi Marina
we are using 5.0.51a without any problem.
Regards, Hans
On 01/24/2011 04:20 PM, Marina Gourtovaia wrote:
Hi
The documentation for _mysql.c for function _mysql_ConnectionObject_ping states that this method assepts an optional parameter. If True, the client will attempt to reconnect. By default this is true in MyQSL<5.0.3 and off thereafter. My version of MySQL is 5.0.51a. Could this be a problem?
Marina
On 21/01/2011 15:45, Marina Gourtovaia wrote:
Hi Nate
It's set to 7200. Changing it to 200 or even to -1(!) does not make any difference.
Marina
On 21/01/2011 15:31, Nate Coraor wrote:
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
-- 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.
Apparently, it's the client that is 5.0.51a; our server version is 5.1.51. Any experience with this one anyone? Marina On 24/01/2011 16:09, Marina Gourtovaia wrote:
Hi Hans
Thanks, good to know. Not sure how to nail this problem...
Marina
On 24/01/2011 16:02, Hans-Rudolf Hotz wrote:
Hi Marina
we are using 5.0.51a without any problem.
Regards, Hans
On 01/24/2011 04:20 PM, Marina Gourtovaia wrote:
Hi
The documentation for _mysql.c for function _mysql_ConnectionObject_ping states that this method assepts an optional parameter. If True, the client will attempt to reconnect. By default this is true in MyQSL<5.0.3 and off thereafter. My version of MySQL is 5.0.51a. Could this be a problem?
Marina
On 21/01/2011 15:45, Marina Gourtovaia wrote:
Hi Nate
It's set to 7200. Changing it to 200 or even to -1(!) does not make any difference.
Marina
On 21/01/2011 15:31, Nate Coraor wrote:
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
-- 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.
Below follows what our DBA did to solve the problem. Also, an article at http://www.webyog.com/blog/2009/09/02/“mysql-server-has-gone-away”-part-2-session-timeout/ explains what MySQL server settings matter. Marina On 26/01/2011 15:32, Karen Ambrose wrote:
Hi Marina,
Here is the solution to the problem.
Checked the global.wait_timeout and session.wait_timeout parameters:
mysql> select @@global.wait_timeout; +-----------------------+ | @@global.wait_timeout | +-----------------------+ | 30 | +-----------------------+ 1 row in set (0.00 sec)
mysql> select @@session.wait_timeout; +------------------------+ | @@session.wait_timeout | +------------------------+ | 28800 | +------------------------+ 1 row in set (0.00 sec)
Once the global wait_timeout was set to 28800 then this worked.
mysql> select @@global.wait_timeout; +-----------------------+ | @@global.wait_timeout | +-----------------------+ | 28800 | +-----------------------+ 1 row in set (0.00 sec)
Regards
Karen
__________________________________________
Karen Ambrose (kva@sanger.ac.uk) Senior Database Administrator Team 106: Database Administration Team
-- 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.
Marina Gourtovaia wrote:
Below follows what our DBA did to solve the problem. Also, an article at http://www.webyog.com/blog/2009/09/02/“mysql-server-has-gone-away”-part-2-session-timeout/ explains what MySQL server settings matter.
Hi Marina, Fantastic, thanks for letting us know the solution. I've added this information to our documentation in the Wiki. --nate
Marina
On 26/01/2011 15:32, Karen Ambrose wrote:
Hi Marina,
Here is the solution to the problem.
Checked the global.wait_timeout and session.wait_timeout parameters:
mysql> select @@global.wait_timeout; +-----------------------+ | @@global.wait_timeout | +-----------------------+ | 30 | +-----------------------+ 1 row in set (0.00 sec)
mysql> select @@session.wait_timeout; +------------------------+ | @@session.wait_timeout | +------------------------+ | 28800 | +------------------------+ 1 row in set (0.00 sec)
Once the global wait_timeout was set to 28800 then this worked.
mysql> select @@global.wait_timeout; +-----------------------+ | @@global.wait_timeout | +-----------------------+ | 28800 | +-----------------------+ 1 row in set (0.00 sec)
Regards
Karen
__________________________________________
Karen Ambrose (kva@sanger.ac.uk) Senior Database Administrator Team 106: Database Administration Team
-- 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
participants (3)
-
Hans-Rudolf Hotz -
Marina Gourtovaia -
Nate Coraor