database I/O error - galaxy-dev

22 Oct 2013


      Hi all,
I have a client who is trying to run velvet on a small bacterial assembly
in Galaxy.  She is using our Core's custom Galaxy in the Amazon Cloud.  It
has had very few problems and we have been updating it and using it for
years.  However, after her assembly ran for a while, Galaxy crashed and now
gives this error whenever you try to access it:
Error Traceback:
⇝ OperationalError: (OperationalError) disk I/O error u'UPDATE
galaxy_session
SET update_time=?, is_valid=? WHERE galaxy_session.id = ?' ['2013-10-17
18:22:49.991937', 0, 110]
URL: http://ec2-54-219-128-159.us-west-1.compute.amazonaws.com/user/logout
Module weberror.evalexception.middleware:364 in respond view
...
...
app_iter = self.application(environ, detect_start_response)
Module paste.debug.prints:98 in __call__ view
...
...
environ, self.app)
Module paste.wsgilib:539 in intercept_output view
...
...
app_iter = application(environ, replacement_start_response)
Module paste.recursive:80 in __call__ view
...
...
return self.application(environ, start_response)
Module paste.httpexceptions:632 in __call__ view
...
...
return self.application(environ, start_response)
Module galaxy.web.framework.base:132 in __call__ view
...
...
return self.handle_request( environ, start_response )
Module galaxy.web.framework.base:185 in handle_request view
...
...
body = method( trans, **kwargs )
Module galaxy.webapps.galaxy.controllers.user:509 in logout view
...
...
trans.handle_user_logout( logout_all=logout_all )
Module galaxy.web.framework:713 in handle_user_logout view
...
...
self.sa_session.flush()
Module sqlalchemy.orm.scoping:127 in do view
...
...
return getattr(self.registry(), name)(*args, **kwargs)
Module sqlalchemy.orm.session:1356 in flush view
...
...
self._flush(objects)
Module sqlalchemy.orm.session:1434 in _flush view
...
...
flush_context.execute()
Module sqlalchemy.orm.unitofwork:261 in execute view
...
...
UOWExecutor().execute(self, tasks)
Module sqlalchemy.orm.unitofwork:753 in execute view
...
...
self.execute_save_steps(trans, task)
Module sqlalchemy.orm.unitofwork:768 in execute_save_steps view
...
...
self.save_objects(trans, task)
Module sqlalchemy.orm.unitofwork:759 in save_objects view
...
...
task.mapper._save_obj(task.polymorphic_tosave_objects, trans)
Module sqlalchemy.orm.mapper:1413 in _save_obj view
...
...
c = connection.execute(statement.values(value_params), params)
Module sqlalchemy.engine.base:824 in execute view
...
...
return Connection.executors[c](self, object, multiparams, params)
Module sqlalchemy.engine.base:874 in _execute_clauseelement view
...
...
return self.__execute_context(context)
Module sqlalchemy.engine.base:896 in __execute_context view
...
...
self._cursor_execute(context.cursor, context.statement,
context.parameters[0], context=context)
Module sqlalchemy.engine.base:950 in _cursor_execute view
...
...
self._handle_dbapi_exception(e, statement, parameters, cursor, context)
Module sqlalchemy.engine.base:931 in _handle_dbapi_exception view
...
...
raise exc.DBAPIError.instance(statement, parameters, e,
connection_invalidated=is_disconnect)
OperationalError: (OperationalError) disk I/O error u'UPDATE galaxy_session
SET
update_time=?, is_valid=? WHERE galaxy_session.id = ?' ['2013-10-17
18:22:49.991937', 0,
110]
I will be getting more information from her soon, but I just wanted to post
this to see if anybody had any suggestions about what might be going on and
perhaps how to fix it?  Any help would be highly appreciated.  Thanks!
- Nik.
-- 
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
najoshi -at- ucdavis -dot- edu
530.752.2698 (w)