How can I profile a multithread program in Python?
Instead of running one cProfile, you could run separate cProfile instance in each thread, then combine the stats. Stats.add() does this automatically.
If you're okay with doing a bit of extra work, you can write your own profiling class that implements profile(self, frame, event, arg). That gets called whenever a function is called, and you can fairly easily set up a structure to gather statistics from that.
You can then use threading.setprofile to register that function on every thread. When the function is called you can use threading.currentThread() to see which it's running on. More information (and ready-to-run recipe) here:
http://code.activestate.com/recipes/465831/
http://docs.python.org/library/threading.html#threading.setprofile