Happened with me too. In m case, nova-cloud-controller is in an LXC container on a beefy machine.
2014-07-04 19:01:48 INFO juju-log shared-db:45: Wrote template /etc/haproxy/haproxy.cfg.
2014-07-04 19:01:48 INFO juju-log shared-db:45: Migrating the nova database.
2014-07-04 19:01:49 INFO shared-db-relation-changed 2014-07-04 19:01:49.908 11320 INFO migrate.versioning.api [-] 215 -> 216... 
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 CRITICAL nova [-] IntegrityError: (IntegrityError) (1062, "Duplicate entry 'juju-machin
e-0-lxc-0-conductor-0' for key 'uniq_services0host0topic0deleted'") 'ALTER TABLE services ADD CONSTRAINT uniq_services0host0topic0deleted UNIQUE (host, topic, deleted)' 
()
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova Traceback (most recent call last):
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova   File "/usr/bin/nova-manage", line 10, in <module>
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova     sys.exit(main())
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova   File "/usr/lib/python2.7/dist-packages/nova/cmd/manage.py", line 1374, in 
main
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova     ret = fn(*fn_args, **fn_kwargs)
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova   File "/usr/lib/python2.7/dist-packages/nova/cmd/manage.py", line 883, in s
ync
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova     return migration.db_sync(version)
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova   File "/usr/lib/python2.7/dist-packages/nova/db/migration.py", line 29, in 
db_sync
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova     return IMPL.db_sync(version=version)
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova   File "/usr/lib/python2.7/dist-packages/nova/db/sqlalchemy/migration.py", l
ine 44, in db_sync
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova     return versioning_api.upgrade(get_engine(), repository, version)
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova   File "/usr/lib/python2.7/dist-packages/migrate/versioning/api.py", line 18
6, in upgrade
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova     return _migrate(url, repository, version, upgrade=True, err=err, **opts)
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova   File "<string>", line 2, in _migrate
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova   File "/usr/lib/python2.7/dist-packages/migrate/versioning/util/__init__.py", line 159, in with_engine
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova     return f(*a, **kw)
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova   File "/usr/lib/python2.7/dist-packages/migrate/versioning/api.py", line 366, in _migrate
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova     schema.runchange(ver, change, changeset.step)
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova   File "/usr/lib/python2.7/dist-packages/migrate/versioning/schema.py", line 91, in runchange
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova     change.run(self.engine, step)
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova   File "/usr/lib/python2.7/dist-packages/migrate/versioning/script/py.py", line 145, in run
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova     script_func(engine)
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova   File "/usr/lib/python2.7/dist-packages/nova/db/sqlalchemy/migrate_repo/versions/216_havana.py", line 1173, in upgrade
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova     name='uniq_services0host0topic0deleted').create()
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova   File "/usr/lib/python2.7/dist-packages/migrate/changeset/constraint.py", line 44, in create
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova     self.__do_imports('constraintgenerator', *a, **kw)
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova   File "/usr/lib/python2.7/dist-packages/migrate/changeset/constraint.py", line 32, in __do_imports
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova     run_single_visitor(engine, visitorcallable, self, *a, **kw)
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova   File "/usr/lib/python2.7/dist-packages/migrate/changeset/databases/visitor.py", line 75, in run_single_visitor
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova     fn(element, **kwargs)
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova   File "/usr/lib/python2.7/dist-packages/migrate/changeset/ansisql.py", line 290, in visit_migrate_unique_constraint
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova     self._visit_constraint(*p, **k)
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova   File "/usr/lib/python2.7/dist-packages/migrate/changeset/ansisql.py", line 296, in _visit_constraint
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova     self.execute()
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova   File "/usr/lib/python2.7/dist-packages/migrate/changeset/ansisql.py", line 43, in execute
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova     return self.connection.execute(self.buffer.getvalue())
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova   File "/usr/lib/python2.7/dist-packages/sqlalchemy/engine/base.py", line 662, in execute
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova     params)
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova   File "/usr/lib/python2.7/dist-packages/sqlalchemy/engine/base.py", line 805, in _execute_text
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova     statement, parameters
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova   File "/usr/lib/python2.7/dist-packages/sqlalchemy/engine/base.py", line 874, in _execute_context
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova     context)
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova   File "/usr/lib/python2.7/dist-packages/sqlalchemy/engine/base.py", line 1024, in _handle_dbapi_exception
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova     exc_info
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova   File "/usr/lib/python2.7/dist-packages/sqlalchemy/util/compat.py", line 196, in raise_from_cause
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova     reraise(type(exception), exception, tb=exc_tb)
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova   File "/usr/lib/python2.7/dist-packages/sqlalchemy/engine/base.py", line 867, in _execute_context
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova     context)
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova   File "/usr/lib/python2.7/dist-packages/sqlalchemy/engine/default.py", line 324, in do_execute
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova     cursor.execute(statement, parameters)
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova   File "/usr/lib/python2.7/dist-packages/MySQLdb/cursors.py", line 174, in execute
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova     self.errorhandler(self, exc, value)
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova   File "/usr/lib/python2.7/dist-packages/MySQLdb/connections.py", line 36, in defaulterrorhandler
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova     raise errorclass, errorvalue
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova IntegrityError: (IntegrityError) (1062, "Duplicate entry 'juju-machine-0-lxc-0-conductor-0' for key 'uniq_services0host0topic0deleted'") 'ALTER TABLE services ADD CONSTRAINT uniq_services0host0topic0deleted UNIQUE (host, topic, deleted)' ()
2014-07-04 19:02:07 INFO shared-db-relation-changed 2014-07-04 19:02:07.057 11320 TRACE nova 
2014-07-04 19:02:07 INFO shared-db-relation-changed Traceback (most recent call last):
2014-07-04 19:02:07 INFO shared-db-relation-changed   File "/var/lib/juju/agents/unit-nova-cloud-controller-0/charm/hooks/shared-db-relation-changed", line 511, in <module>
2014-07-04 19:02:07 INFO shared-db-relation-changed     main()
2014-07-04 19:02:07 INFO shared-db-relation-changed   File "/var/lib/juju/agents/unit-nova-cloud-controller-0/charm/hooks/shared-db-relation-changed", line 505, in main
2014-07-04 19:02:07 INFO shared-db-relation-changed     hooks.execute(sys.argv)
2014-07-04 19:02:07 INFO shared-db-relation-changed   File "/var/lib/juju/agents/unit-nova-cloud-controller-0/charm/hooks/charmhelpers/core/hookenv.py", line 478, in execute
2014-07-04 19:02:07 INFO shared-db-relation-changed     self._hooks[hook_name]()
2014-07-04 19:02:07 INFO shared-db-relation-changed   File "/var/lib/juju/agents/unit-nova-cloud-controller-0/charm/hooks/charmhelpers/core/host.py", line 218, in wrapped_f
2014-07-04 19:02:07 INFO shared-db-relation-changed     f(*args)
2014-07-04 19:02:07 INFO shared-db-relation-changed   File "/var/lib/juju/agents/unit-nova-cloud-controller-0/charm/hooks/shared-db-relation-changed", line 182, in db_changed
2014-07-04 19:02:07 INFO shared-db-relation-changed     migrate_database()
2014-07-04 19:02:07 INFO shared-db-relation-changed   File "/var/lib/juju/agents/unit-nova-cloud-controller-0/charm/hooks/nova_cc_utils.py", line 485, in migrate_database
2014-07-04 19:02:07 INFO shared-db-relation-changed     subprocess.check_output(cmd)
2014-07-04 19:02:07 INFO shared-db-relation-changed   File "/usr/lib/python2.7/subprocess.py", line 573, in check_output
2014-07-04 19:02:07 INFO shared-db-relation-changed     raise CalledProcessError(retcode, cmd, output=output)
2014-07-04 19:02:07 INFO shared-db-relation-changed subprocess.CalledProcessError: Command '['nova-manage', 'db', 'sync']' returned non-zero exit status 1
2014-07-04 19:02:07 ERROR juju.worker.uniter uniter.go:486 hook failed: exit status 1