After applying fix [1], still seeing error where original exception is replaced with another one in rollback block [2].
This is where original analysis(from ticket description) applies. So fix [3] is still needed.

2016-04-19 00:50:30.716 18062 ERROR neutron.db.ipam_pluggable_backend [req-0ed5f0d8-42a0-47e4-89e2-bdf6fef3e1dc tempest-PortsTestJSON-447574898 -] IP deallocation failed on external system for 10.100.0.5, 10.100.0.20
2016-04-19 00:50:30.726 18062 ERROR root [req-0ed5f0d8-42a0-47e4-89e2-bdf6fef3e1dc tempest-PortsTestJSON-447574898 -] Original exception being dropped: ['Traceback (most recent call last):\n', '  File "/opt/stack/new/neutron/neutron/db/ipam_pluggable_backend.py", line 310, in update_port_with_ips\n    ip[\'subnet_id\'], ip[\'ip_address\'])\n', '  File "/opt/stack/new/neutron/neutron/db/db_base_plugin_common.py", line 92, in _delete_ip_allocation\n    subnet_id=subnet_id).delete()\n', '  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/orm/query.py", line 3048, in delete\n    delete_op.exec_()\n', '  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/orm/persistence.py", line 1125, in exec_\n    self._do_pre()\n', '  File "<string>", line 1, in <lambda>\n', '  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/orm/persistence.py", line 1163, in _do_pre\n    session._autoflush()\n', '  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/orm/session.py", line 1293, in _autoflush\n    self.flush()\n', '  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/orm/session.py", line 2019, in flush\n    self._flush(objects)\n', '  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/orm/session.py", line 2137, in _flush\n    transaction.rollback(_capture_exception=True)\n', '  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/util/langhelpers.py", line 60, in __exit__\n    compat.reraise(exc_type, exc_value, exc_tb)\n', '  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/orm/session.py", line 2101, in _flush\n    flush_context.execute()\n', '  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/orm/unitofwork.py", line 373, in execute\n    rec.execute(self)\n', '  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/orm/unitofwork.py", line 532, in execute\n    uow\n', '  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/orm/persistence.py", line 174, in save_obj\n    mapper, table, insert)\n', '  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/orm/persistence.py", line 767, in _emit_insert_statements\n    execute(statement, multiparams)\n', '  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/engine/base.py", line 914, in execute\n    return meth(self, multiparams, params)\n', '  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/sql/elements.py", line 323, in _execute_on_connection\n    return connection._execute_clauseelement(self, multiparams, params)\n', '  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/engine/base.py", line 1010, in _execute_clauseelement\n    compiled_sql, distilled_params\n', '  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/engine/base.py", line 1146, in _execute_context\n    context)\n', '  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/engine/base.py", line 1337, in _handle_dbapi_exception\n    util.raise_from_cause(newraise, exc_info)\n', '  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/util/compat.py", line 200, in raise_from_cause\n    reraise(type(exception), exception, tb=exc_tb, cause=cause)\n', '  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/engine/base.py", line 1139, in _execute_context\n    context)\n', '  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/engine/default.py", line 450, in do_execute\n    cursor.execute(statement, parameters)\n', '  File "/usr/local/lib/python2.7/dist-packages/pymysql/cursors.py", line 158, in execute\n    result = self._query(query)\n', '  File "/usr/local/lib/python2.7/dist-packages/pymysql/cursors.py", line 308, in _query\n    conn.query(q)\n', '  File "/usr/local/lib/python2.7/dist-packages/pymysql/connections.py", line 820, in query\n    self._affected_rows = self._read_query_result(unbuffered=unbuffered)\n', '  File "/usr/local/lib/python2.7/dist-packages/pymysql/connections.py", line 1002, in _read_query_result\n    result.read()\n', '  File "/usr/local/lib/python2.7/dist-packages/pymysql/connections.py", line 1285, in read\n    first_packet = self.connection._read_packet()\n', '  File "/usr/local/lib/python2.7/dist-packages/pymysql/connections.py", line 966, in _read_packet\n    packet.check_error()\n', '  File "/usr/local/lib/python2.7/dist-packages/pymysql/connections.py", line 394, in check_error\n    err.raise_mysql_exception(self._data)\n', '  File "/usr/local/lib/python2.7/dist-packages/pymysql/err.py", line 120, in raise_mysql_exception\n    _check_mysql_exception(errinfo)\n', '  File "/usr/local/lib/python2.7/dist-packages/pymysql/err.py", line 115, in _check_mysql_exception\n    raise InternalError(errno, errorvalue)\n', "DBDeadlock: (pymysql.err.InternalError) (1213, u'Deadlock found when trying to get lock; try restarting transaction') [SQL: u'INSERT INTO ipamallocations (ip_address, status, ipam_subnet_id) VALUES (%(ip_address)s, %(status)s, %(ipam_subnet_id)s)'] [parameters: {'status': 'ALLOCATED', 'ip_address': u'10.100.0.20', 'ipam_subnet_id': u'51995705-2d27-436d-9e93-f666484cb302'}]\n"]
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource [req-0ed5f0d8-42a0-47e4-89e2-bdf6fef3e1dc tempest-PortsTestJSON-447574898 -] update failed
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource Traceback (most recent call last):
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource   File "/opt/stack/new/neutron/neutron/api/v2/resource.py", line 84, in resource
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource     result = method(request=request, **args)
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource   File "/opt/stack/new/neutron/neutron/api/v2/base.py", line 579, in update
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource     return self._update(request, id, body, **kwargs)
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource   File "/usr/local/lib/python2.7/dist-packages/oslo_db/api.py", line 148, in wrapper
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource     ectxt.value = e.inner_exc
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource   File "/usr/local/lib/python2.7/dist-packages/oslo_utils/excutils.py", line 220, in __exit__
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource     self.force_reraise()
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource   File "/usr/local/lib/python2.7/dist-packages/oslo_utils/excutils.py", line 196, in force_reraise
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource     six.reraise(self.type_, self.value, self.tb)
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource   File "/usr/local/lib/python2.7/dist-packages/oslo_db/api.py", line 138, in wrapper
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource     return f(*args, **kwargs)
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource   File "/opt/stack/new/neutron/neutron/api/v2/base.py", line 624, in _update
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource     obj = obj_updater(request.context, id, **kwargs)
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource   File "/opt/stack/new/neutron/neutron/plugins/ml2/plugin.py", line 1215, in update_port
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource     port)
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource   File "/opt/stack/new/neutron/neutron/db/db_base_plugin_v2.py", line 1296, in update_port
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource     new_port, new_mac)
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource   File "/opt/stack/new/neutron/neutron/db/ipam_pluggable_backend.py", line 322, in update_port_with_ips
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource     revert_on_fail=False)
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource   File "/opt/stack/new/neutron/neutron/db/ipam_pluggable_backend.py", line 75, in _ipam_deallocate_ips
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource     "external system for %s"), addresses)
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource   File "/usr/local/lib/python2.7/dist-packages/oslo_utils/excutils.py", line 220, in __exit__
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource     self.force_reraise()
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource   File "/usr/local/lib/python2.7/dist-packages/oslo_utils/excutils.py", line 196, in force_reraise
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource     six.reraise(self.type_, self.value, self.tb)
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource   File "/opt/stack/new/neutron/neutron/db/ipam_pluggable_backend.py", line 58, in _ipam_deallocate_ips
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource     ipam_subnet = ipam_driver.get_subnet(ip['subnet_id'])
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource   File "/opt/stack/new/neutron/neutron/ipam/drivers/neutrondb_ipam/driver.py", line 401, in get_subnet
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource     return NeutronDbSubnet.load(subnet_id, self._context)
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource   File "/opt/stack/new/neutron/neutron/ipam/drivers/neutrondb_ipam/driver.py", line 94, in load
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource     ctx.session, neutron_subnet_id)
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource   File "/opt/stack/new/neutron/neutron/ipam/drivers/neutrondb_ipam/db_api.py", line 31, in load_by_neutron_subnet_id
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource     neutron_subnet_id=neutron_subnet_id).first()
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource   File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/orm/query.py", line 2634, in first
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource     ret = list(self[0:1])
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource   File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/orm/query.py", line 2457, in __getitem__
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource     return list(res)
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource   File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/orm/query.py", line 2736, in __iter__
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource     return self._execute_and_instances(context)
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource   File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/orm/query.py", line 2749, in _execute_and_instances
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource     close_with_result=True)
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource   File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/orm/query.py", line 2740, in _connection_from_session
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource     **kw)
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource   File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/orm/session.py", line 893, in connection
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource     execution_options=execution_options)
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource   File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/orm/session.py", line 898, in _connection_for_bind
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource     engine, execution_options)
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource   File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/orm/session.py", line 313, in _connection_for_bind
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource     self._assert_active()
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource   File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/orm/session.py", line 214, in _assert_active
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource     % self._rollback_exception
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource InvalidRequestError: This Session's transaction has been rolled back due to a previous exception during flush. To begin a new transaction with this Session, first issue Session.rollback(). Original exception was: (pymysql.err.InternalError) (1213, u'Deadlock found when trying to get lock; try restarting transaction') [SQL: u'INSERT INTO ipamallocations (ip_address, status, ipam_subnet_id) VALUES (%(ip_address)s, %(status)s, %(ipam_subnet_id)s)'] [parameters: {'status': 'ALLOCATED', 'ip_address': u'10.100.0.20', 'ipam_subnet_id': u'51995705-2d27-436d-9e93-f666484cb302'}]
2016-04-19 00:50:30.727 18062 ERROR neutron.api.v2.resource

[1] https://review.openstack.org/307329
[2] http://logs.openstack.org/23/181023/67/check/gate-tempest-dsvm-neutron-full/a146aeb/logs/screen-q-svc.txt.gz#_2016-04-19_00_50_30_716
[3] https://review.openstack.org/#/c/306519/