Links between switches not discovered when running integration base distro with OF 1.3 plugin

I am trying to run ODL with OpenFlow 1.3 md-sal plugin from the integration project. I ran the base distro in integration as the wiki says "./run.sh -of13", and in mininet, I set up a small network with "sudo mn --topo tree,2 --switch ovsk,protocols=OpenFlow13 --controller remote,[localhost-ip]".

When I did pingall, I found that hosts that are attached to the same switch can ping each other just fine, but there are no links discovered between switches. When I tried to do "h1 ping h3" where h1 is attached to switch1 and h3 is attached to switch3, the packets are dropped as punted.

Below is the log file, and I've highlighted several warnings and exceptions. From the looks of it, the OF1.3 md-sal plugin is still calling ad-sal SimpleForwardingManagerImpl and I am not seeing hosttracker component.

Any idea why this is and how I could fix the issue? I checked a few related bugs but the fixes don't seem to apply.

Thank you!
Xiao

$ ./run.sh -of13
find: `./configuration/initial.available': No such file or directory
JVM maximum memory was set to -Xmx1G.
osgi> 2014-12-03 22:57:16.358 EST [fileinstall-./plugins] INFO o.o.c.c.s.internal.ClusterManager - I'm a GossipRouter will listen on port 12001
2014-12-03 22:57:16.591 EST [fileinstall-./plugins] INFO o.o.c.c.s.internal.ClusterManager - Started GossipRouter
2014-12-03 22:57:16.592 EST [fileinstall-./plugins] INFO o.o.c.c.s.internal.ClusterManager - Starting the ClusterManager
GossipRouter started at Wed Dec 03 22:57:16 EST 2014
Listening on port 12001 bound on address 0.0.0.0/0.0.0.0
Backlog is 1000, linger timeout is 2000, and read timeout is 0
2014-12-03 22:57:35.342 EST [fileinstall-./plugins] INFO o.o.c.c.i.ConfigurationService - ConfigurationService Manager init
2014-12-03 22:57:36.474 EST [fileinstall-./plugins] WARN o.o.c.u.internal.UserManager - Network Administrator password is set to factory default. Please change the password as soon as possible.
2014-12-03 22:57:47 EST [org.apache.catalina.mbeans.GlobalResourcesLifecycleListener] SEVERE org.apache.catalina.mbeans.GlobalResourcesLifecycleListener createMBeans No global naming context defined for server
2014-12-03 22:57:48.138 EST [config-pusher] INFO o.o.y.y.d.i.s.tree.InMemoryDataTree - Attempting to install schema contexts
2014-12-03 22:57:48.153 EST [config-pusher] INFO o.o.c.m.s.c.u.j.ThreadExecutorStatsMXBeanImpl - Executor com.google.common.util.concurrent.MoreExecutors$SameThreadExecutorService@8ac7447 is not supported
2014-12-03 22:57:48.154 EST [config-pusher] INFO o.o.y.y.d.i.s.tree.InMemoryDataTree - Attempting to install schema contexts
2014-12-03 22:57:48.155 EST [config-pusher] INFO o.o.c.m.s.c.u.j.ThreadExecutorStatsMXBeanImpl - Executor com.google.common.util.concurrent.MoreExecutors$SameThreadExecutorService@214f7dd0 is not supported
2014-12-03 22:57:48.206 EST [config-pusher] INFO o.o.c.m.s.b.i.ForwardedBackwardsCompatibleDataBroker - ForwardedBackwardsCompatibleBroker started.
2014-12-03 22:57:48.221 EST [config-pusher] WARN o.o.c.s.b.i.c.d.BindingIndependentConnector - Unable to start Notification forwarding. Reason: DOM Notification Service is not initialized properly!
2014-12-03 22:57:48.222 EST [config-pusher] INFO o.o.c.s.b.i.RootBindingAwareBroker - Starting Binding Aware Broker: binding-broker-impl
2014-12-03 22:57:51.028 EST [pool-2-thread-1] INFO o.o.controller.frm.FRMActivator - FRMActivator initialization.
2014-12-03 22:57:51.313 EST [pool-2-thread-1] INFO o.o.c.f.i.ForwardingRulesManagerImpl - ForwardingRulesManager has started successfull.
2014-12-03 22:57:51.313 EST [pool-2-thread-1] INFO o.o.controller.frm.FRMActivator - FRMActivator initialization successfull.
2014-12-03 22:57:51.323 EST [config-pusher] INFO o.o.c.s.c.topology.TopologyProvider - TopologyProvider started
2014-12-03 22:57:51.349 EST [pool-2-thread-4] INFO o.o.c.m.s.m.StatisticsManagerActivator - StatisticsManagerActivator initialization.
2014-12-03 22:57:51.378 EST [pool-2-thread-3] INFO o.o.m.c.t.lldp.LLDPDiscoveryProvider - LLDPDiscoveryListener Started.
2014-12-03 22:57:51.391 EST [pool-2-thread-2] INFO o.o.c.m.i.m.FlowCapableInventoryProvider - Flow Capable Inventory Provider started.
2014-12-03 22:57:51.726 EST [config-pusher] INFO o.o.c.c.y.c.k.i.KitchenServiceModule - KitchenService (instance org.opendaylight.controller.config.yang.config.kitchen_service.impl.KitchenServiceModule$1AutoCloseableKitchenService@13c5a945) initialized.
2014-12-03 22:57:51.824 EST [pool-2-thread-4] INFO o.o.c.m.s.m.i.StatisticsManagerImpl - Statistics Manager started successfully!
2014-12-03 22:57:51.824 EST [pool-2-thread-4] INFO o.o.c.m.s.m.StatisticsManagerActivator - StatisticsManagerActivator started successfully.
2014-12-03 22:57:51.831 EST [config-pusher] INFO o.o.c.c.y.c.t.i.ToasterProviderModule - Toaster provider (instance org.opendaylight.controller.config.yang.config.toaster_provider.impl.ToasterProviderModule$1AutoCloseableToaster@229865ac) initialized.
2014-12-03 22:57:52.052 EST [Web socket server on port PortNumber [_value=8185]] INFO o.o.c.s.s.websockets.WebSocketServer - Web socket server started at port 8185.
2014-12-03 22:57:52.204 EST [config-pusher] INFO o.o.y.g.v.u.o.p.x.n.y.o._.c.p.i.rev140328.SwitchConnectionProviderModule - SwitchConnectionProvider started.
2014-12-03 22:57:52.300 EST [config-pusher] INFO o.o.y.g.v.u.o.p.x.n.y.o._.c.p.i.rev140328.SwitchConnectionProviderModule - SwitchConnectionProvider started.
2014-12-03 22:57:52.476 EST [Thread-20] INFO o.o.o.protocol.impl.core.TcpHandler - Switch listener started and ready to accept incoming tcp/tls connections on port: 6633
2014-12-03 22:57:52.479 EST [Thread-21] INFO o.o.o.protocol.impl.core.TcpHandler - Switch listener started and ready to accept incoming tcp/tls connections on port: 6653
2014-12-03 22:57:52.571 EST [config-pusher] INFO o.o.y.g.v.u.o.p.x.n.y.o.c.c.i.r.MsgSpyServiceModule - MsgStatService (instance org.opendaylight.yang.gen.v1.urn.opendaylight.params.xml.ns.yang.openflow.common.config.impl.rev140326.MsgSpyServiceModule$1AutoClosableMsgSpyService@cddb7d2) initialized.
2014-12-03 22:58:00 EST [com.sun.jersey.core.spi.component.ProviderServices] SEVERE com.sun.jersey.core.spi.component.ProviderServices getInstances The class org.opendaylight.aaa.sts.TokenAuthFilter could not be found. This class is ignored.
2014-12-03 22:58:01 EST [com.sun.jersey.spi.inject.Errors] WARNING com.sun.jersey.spi.inject.Errors processErrorMessages The following warnings have been detected with resource and/or provider classes:
WARNING: Parameter 2 of type org.opendaylight.yangtools.yang.data.api.Node<?> from public abstract javax.ws.rs.core.Response org.opendaylight.controller.sal.rest.api.RestconfService.updateConfigurationData(java.lang.String,org.opendaylight.yangtools.yang.data.api.Node<?>) is not resolvable to a concrete type
WARNING: Parameter 2 of type org.opendaylight.yangtools.yang.data.api.Node<?> from public abstract javax.ws.rs.core.Response org.opendaylight.controller.sal.rest.api.RestconfService.createConfigurationData(java.lang.String,org.opendaylight.yangtools.yang.data.api.Node<?>) is not resolvable to a concrete type
WARNING: Parameter 1 of type org.opendaylight.yangtools.yang.data.api.Node<?> from public abstract javax.ws.rs.core.Response org.opendaylight.controller.sal.rest.api.RestconfService.createConfigurationData(org.opendaylight.yangtools.yang.data.api.Node<?>) is not resolvable to a concrete type
2014-12-03 22:58:29.491 EST [remote-connector-processing-executor-3] WARN o.o.c.s.c.n.s.NetconfDeviceSalFacade - RemoteDevice

{controller-config}: Some rpcs from netconf device were not registered: [(urn:opendaylight:group:service?revision=2013-09-18)add-group, (urn:opendaylight:port:statistics?revision=2013-12-14)get-all-node-connectors-statistics, (urn:opendaylight:meter:statistics?revision=2013-11-11)get-meter-features, (urn:opendaylight:meter:service?revision=2013-09-18)add-meter, (urn:opendaylight:flow:statistics?revision=2013-08-19)get-aggregate-flow-statistics-from-flow-table-for-given-match, (urn:opendaylight:flow:service?revision=2013-08-19)remove-flow, (urn:opendaylight:group:statistics?revision=2013-11-11)get-group-features, (urn:opendaylight:group:statistics?revision=2013-11-11)get-all-group-statistics, (urn:opendaylight:flow:table:statistics?revision=2013-12-15)get-flow-tables-statistics, (urn:opendaylight:queue:statistics?revision=2013-12-16)get-queue-statistics-from-given-port, (urn:opendaylight:group:statistics?revision=2013-11-11)get-group-statistics, (urn:opendaylight:group:service?revision=2013-09-18)remove-group, (urn:opendaylight:flow:statistics?revision=2013-08-19)get-aggregate-flow-statistics-from-flow-table-for-all-flows, (urn:opendaylight:flow:service?revision=2013-08-19)update-flow, (urn:opendaylight:flow:statistics?revision=2013-08-19)get-all-flow-statistics-from-flow-table, (urn:opendaylight:port:statistics?revision=2013-12-14)get-node-connector-statistics, (urn:opendaylight:flow:transaction?revision=2013-11-03)get-next-transaction-id, (urn:opendaylight:table:service?revision=2013-10-26)update-table, (urn:opendaylight:port:service?revision=2013-11-07)update-port, (urn:opendaylight:flow:service?revision=2013-08-19)add-flow, (urn:opendaylight:queue:statistics?revision=2013-12-16)get-all-queues-statistics-from-all-ports, (urn:opendaylight:meter:statistics?revision=2013-11-11)get-meter-statistics, (urn:opendaylight:meter:service?revision=2013-09-18)remove-meter, (urn:opendaylight:meter:service?revision=2013-09-18)update-meter, (urn:opendaylight:group:statistics?revision=2013-11-11)get-group-description, (urn:opendaylight:group:service?revision=2013-09-18)update-group, (urn:opendaylight:packet:service?revision=2013-07-09)transmit-packet, (urn:opendaylight:meter:statistics?revision=2013-11-11)get-all-meter-statistics, (urn:opendaylight:meter:statistics?revision=2013-11-11)get-all-meter-config-statistics, (urn:opendaylight:module:config?revision=2014-10-15)set-config, (urn:opendaylight:flow:statistics?revision=2013-08-19)get-all-flows-statistics-from-all-flow-tables, (urn:opendaylight:queue:statistics?revision=2013-12-16)get-all-queues-statistics-from-given-port, (urn:opendaylight:flow:statistics?revision=2013-08-19)get-flow-statistics-from-flow-table, (urn:opendaylight:flow:transaction?revision=2013-11-03)finish-transaction]
2014-12-03 22:58:33.127 EST [remote-connector-processing-executor-3] INFO o.o.c.s.c.netconf.NetconfDevice - RemoteDevice{controller-config}

: Netconf connector initialized successfully

2014-12-03 22:58:51.226 EST [nioEventLoopGroup-11-1] WARN o.o.o.o.m.c.s.SessionManagerOFImpl - context for invalidation not found
2014-12-03 22:58:51.316 EST [OFHandshake-0-0] WARN o.o.o.o.m.c.ErrorHandlerSimpleImpl - exception -> FIRST HELLO sending failed because of connection issue., session -> null
org.opendaylight.openflowplugin.ConnectionException: FIRST HELLO sending failed because of connection issue.
at org.opendaylight.openflowplugin.openflow.md.core.HandshakeManagerImpl.sendHelloMessage(HandshakeManagerImpl.java:297) ~[bundlefile:na]
at org.opendaylight.openflowplugin.openflow.md.core.HandshakeManagerImpl.shake(HandshakeManagerImpl.java:98) ~[bundlefile:na]
at org.opendaylight.openflowplugin.openflow.md.core.HandshakeStepWrapper.run(HandshakeStepWrapper.java:47) [bundlefile:na]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) [na:1.7.0_65]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) [na:1.7.0_65]
at java.lang.Thread.run(Thread.java:745) [na:1.7.0_65]
2014-12-03 22:58:51.929 EST [nioEventLoopGroup-11-2] INFO o.o.o.p.i.c.c.ConnectionAdapterImpl - Hello received / branch
2014-12-03 22:58:52.296 EST [nioEventLoopGroup-11-3] INFO o.o.o.p.i.c.c.ConnectionAdapterImpl - Hello received / branch
2014-12-03 22:58:52.309 EST [nioEventLoopGroup-11-4] INFO o.o.o.p.i.c.c.ConnectionAdapterImpl - Hello received / branch
2014-12-03 22:58:52.365 EST [nioEventLoopGroup-11-3] WARN o.o.o.o.m.c.s.SessionManagerOFImpl - context for invalidation not found
2014-12-03 22:58:52.365 EST [OFHandshake-2-0] WARN o.o.o.o.m.c.ErrorHandlerSimpleImpl - exception -> FIRST HELLO sending failed because of connection issue., session -> null
org.opendaylight.openflowplugin.ConnectionException: FIRST HELLO sending failed because of connection issue.
at org.opendaylight.openflowplugin.openflow.md.core.HandshakeManagerImpl.sendHelloMessage(HandshakeManagerImpl.java:297) ~[bundlefile:na]
at org.opendaylight.openflowplugin.openflow.md.core.HandshakeManagerImpl.shake(HandshakeManagerImpl.java:98) ~[bundlefile:na]
at org.opendaylight.openflowplugin.openflow.md.core.HandshakeStepWrapper.run(HandshakeStepWrapper.java:47) [bundlefile:na]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) [na:1.7.0_65]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) [na:1.7.0_65]
at java.lang.Thread.run(Thread.java:745) [na:1.7.0_65]
2014-12-03 22:58:53.370 EST [nioEventLoopGroup-11-5] INFO o.o.o.p.i.c.c.ConnectionAdapterImpl - Hello received / branch
2014-12-03 22:59:00.094 EST [Thread-31] WARN o.o.c.s.s.i.SimpleForwardingImpl - Dropping punted IP packet received at OF|1@OF|00:00:00:00:00:00:00:02 to Host /10.0.0.3