I have been facing the same issue for a long time as well: PyCharm debugging is extremely slow when using large pandas dataframes. If I want to view the contents of a dataframe in the Watches is often gives me a time out after waiting for minutes, so I basically stopped using the debug when working with dataframes
What I just found however, it that under
Files -> Settinggs -> Build, Execution, Deployment -> Python Debugger
You have to switch on the “Gevent Compatible” flag
I also have switched on all the other flags in this window (Collect rum-time types information, attach subprocess, and PyQt compatible). But the Gevent compatible flag really does the job for me: it suddenly instantanuously gives me the dataframe contents in the debugger watches.
I am using PyCharm verion 2016.2.3