The problem here is that you are trying to use sys.stdin for two different purposes: 1. as a data input source for your program using stdin redirected to a disk file; and 2. for pdb's source of debugging commands, expected to be a terminal file.  By specifying "-m pdb", you are telling pdb to start an interactive debugging which it does, paused at the first statement in sample.py ("-> import sys, pdb").  It (actually the cmd standard library module which pdb uses) then tries to read stdin for command input but, because of the command line redirect (" < binary.exe"), reads the binary file instead.  Note this happens before sample.py has done anything.  If you just ran the command "python sample.py < binary.exe", then pdb would not be involved initially, the script would run, read the redirected file until EOF, and then invoke pdb via set_trace.  But, at that point, the redirected sys.stdin is at EOF so pdb immediately exits after trying to read a command.  The doc page for pdb does not specifically warn against redirecting stdin but it does document that the pdb.Pdb instance passes stdin arguments to a cmd.Cmd instance which defaults to using sys.stdin.  I think that's warning enough.

There is an open pdb feature request, Issue20061, to make it more convenient to use pdb with a separate terminal window.  That feature would also cover the rare use case here of having a redirected stdin with pdb.  Otherwise, you need to be careful how you use stdin while using pdb.