
Bigger image
Especially I run code perhaps running a little long time(
I had a similar thing happen to me a few months ago, it turned out I had a really slow operation within a __repr__() for a variable I had on the stack. When PyCharm hits a breakpoint it grabs all of the variables in the current scope and calls __repr__ on them. Here's an amusement that demonstrates this issue:
import time
class Foo(object):
def __repr__(self):
time.sleep(100)
return "look at me"
if __name__ == '__main__':
a = Foo()
print "set your breakpoint here"
PyCharm will also call __getattribute__('__class__'). If you have a __getattribute__ that's misbehaving that could trip you up as well.
This may not be what's happening to you but perhaps worth considering.