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.
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--
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. _______________________________________________
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