minor fixes to allow kernel to be re-entrant

* user_mod doesn't typecheck ModuleType, because it can be a DummyMod
* start hearbeat thread in initialize step, not start.
* ensure shell.exit_now is False at Kernel.start

IPython/zmq/ipkernel.py

@@ -84,7 +84,7 b' class Kernel(Configurable):'
     stdin_socket = Instance(zmq.Socket)
     log = Instance(logging.Logger)
     
-    user_module = Instance('types.ModuleType')
+    user_module = Any()
     def _user_module_changed(self, name, old, new):
         if self.shell is not None:
             self.shell.user_module = new
@@ -250,6 +250,7 b' class Kernel(Configurable):'
 
     def start(self):
         """register dispatchers for streams"""
+        self.shell.exit_now = False
         if self.control_stream:
             self.control_stream.on_recv(self.dispatch_control, copy=False)
 
@@ -501,7 +502,8 b' class Kernel(Configurable):'
 
         self._at_shutdown()
         # call sys.exit after a short delay
-        ioloop.IOLoop.instance().add_timeout(time.time()+0.1, lambda : sys.exit(0))
+        loop = ioloop.IOLoop.instance()
+        loop.add_timeout(time.time()+0.1, loop.stop)
 
     #---------------------------------------------------------------------------
     # Engine methods

IPython/zmq/kernelapp.py

@@ -225,6 +225,7 b' class KernelApp(BaseIPythonApplication):'
         self.heartbeat = Heartbeat(hb_ctx, (self.ip, self.hb_port))
         self.hb_port = self.heartbeat.port
         self.log.debug("Heartbeat REP Channel on port: %i"%self.hb_port)
+        self.heartbeat.start()
 
         # Helper to make it easier to connect to an existing kernel.
         # set log-level to critical, to make sure it is output
@@ -302,7 +303,6 b' class KernelApp(BaseIPythonApplication):'
         sys.stderr.flush()
 
     def start(self):
-        self.heartbeat.start()
         if self.poller is not None:
             self.poller.start()
         self.kernel.start()