When running program which reads from stdio from in bash, I can signal EOF by typing Ctrl-D. When debugging such a program in gdb mode in Emacs, Ctl-D is not recognized in the input/output window. I am running Ubuntu 16.04.
If you're running it from shell, then either try to press C-c C-d that will call comint-send-eof function, or if it's really inside program itself, you can try to use C-q C-d to send C-d as raw key command.
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