KeyError in module 'threading' after a successful py.test run

I observed a similar issue and decided to see what's going on exactly - let me describe my findings. I hope someone will find it useful. Short story It is indeed related to monkey-patching the threading module. In fact, I can easily trigger the exception by importing the threading module before monkey-patching threads. The following 2 lines are enough: import threading import gevent.monkey; gevent.monkey.patch_thread() When executed it spits the message about ignored KeyError: (env)czajnik@autosan:~$ python test.py Exception KeyError: KeyError(139924387112272,) in <module 'threading' from '/usr/lib/python2.7/threading.pyc'> ignored If you swap the import lines, the problem is gone. Long story I could stop my debugging here, but I decided it's worth to understand the exact cause of the problem. First step was to find the code that prints the message about ignored exception. It was a little hard for me to find it (grepping for Exception.*ignored yielded nothing), but grepping around CPython source code I've eventually found a function called void PyErr_WriteUnraisable(PyObject *obj) in Python/error.c, with a very interesting comment: /* Call when an exception has occurred but there is no way for Python to handle it. Examples: exception in __del__ or during GC. */ I decided to check who's calling it, with a little help from gdb, just to get the following C-level stack trace: #0 0x0000000000542c40 in PyErr_WriteUnraisable () #1 0x00000000004af2d3 in Py_Finalize () #2 0x00000000004aa72e in Py_Main () #3 0x00007ffff68e576d in __libc_start_main (main=0x41b980 <main>, argc=2, ubp_av=0x7fffffffe5f8, init=<optimized out>, fini=<optimized out>, rtld_fini=<optimized out>, stack_end=0x7fffffffe5e8) at libc-start.c:226 #4 0x000000000041b9b1 in _start () Now we can clearly see that the exception is thrown while Py_Finalize executes - this call is responsible for shutting down the Python interpreter, freeing allocated memory, etc. It's called just before exitting. Next step was to look at Py_Finalize() code (it's in Python/pythonrun.c). The very first call it makes is wait_for_thread_shutdown() - worth looking at, as we know the problem is related to threading. This function in turn calls _shutdown callable in the threading module. Good, we can go back to python code now. Looking at threading.py I've found the following interesting parts: class _MainThread(Thread): def _exitfunc(self): self._Thread__stop() t = _pickSomeNonDaemonThread() if t: if __debug__: self._note("%s: waiting for other threads", self) while t: t.join() t = _pickSomeNonDaemonThread() if __debug__: self._note("%s: exiting", self) self._Thread__delete() # Create the main thread object, # and make it available for the interpreter # (Py_Main) as threading._shutdown. _shutdown = _MainThread()._exitfunc Clearly, the responsibility of threading._shutdown() call is to join all non-daemon threads and delete main thread (whatever that means exactly). I decided to patch threading.py a bit - wrap the whole _exitfunc() body with try/except and print the stack trace with traceback module. This gave the following trace: Traceback (most recent call last): File "/usr/lib/python2.7/threading.py", line 785, in _exitfunc self._Thread__delete() File "/usr/lib/python2.7/threading.py", line 639, in __delete del _active[_get_ident()] KeyError: 26805584 Now we know the exact place where the exception is thrown - inside Thread.__delete() method. The rest of the story is obvious after reading threading.py for a while. The _active dictionary maps thread IDs (as returned by _get_ident()) to Thread instances, for all threads created. When threading module is loaded, an instance of _MainThread class is always created and added to _active (even if no other threads are explicitly created). The problem is that one of the methods patched by gevent's monkey-patching is _get_ident() - original one maps to thread.get_ident(), monkey-patching replaces it with green_thread.get_ident(). Obviously both calls return different IDs for main thread. Now, if threading module is loaded before monkey-patching, _get_ident() call returns one value when _MainThread instance is created and added to _active, and another value at the time _exitfunc() is called - hence KeyError in del _active[_get_ident()]. On the contrary, if monkey-patching is done before threading is loaded, all is fine - at the time _MainThread instance is being added to _active, _get_ident() is already patched, and the same thread ID is returned at cleanup time. That's it! To make sure I import modules in the right order, I added the following snippet to my code, just before monkey-patching call: import sys if 'threading' in sys.modules: raise Exception('threading module loaded before patching!') import gevent.monkey; gevent.monkey.patch_thread() I hope you find my debugging story useful :)