gdb (test version) and program's 'read' seem to have an input clash.
Anyway, gdb used to pause and allow keyboard input.

With test fortran program:
      program foo
      implicit none
      real*4 e /0.0/
      write(*,*) "Enter a real number"
      read(*,*) e
      write (*,*) "e =", e

$ /usr/bin/gfortran    -g foo.f -o foo

$ gdb foo
GNU gdb (GDB) (Cygwin 7.11.1-1) 7.11.1
Copyright (C) 2016 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "i686-pc-cygwin".
Type "show configuration" for configuration details.
For bug reporting instructions, please see:
Find the GDB manual and other documentation resources online at:
For help, type "help".
Type "apropos word" to search for commands related to "word"...
Reading symbols from foo...done.
(gdb) b 1
Breakpoint 1 at 0x4011d9: file foo.f, line 1.
(gdb) r
Starting program: /cygdrive/c/Users/harryr/d62/EMBL500/svn/EMBL500/foo
[New Thread 4296.0xb90]
[New Thread 4296.0x1d78]
[New Thread 4296.0x181c]
[New Thread 4296.0x1738]

Thread 1 "foo" hit Breakpoint 1, foo () at foo.f:4
4             write(*,*) "Enter a real number"
(gdb) n
 Enter a real number
5             read(*,*) e
(gdb) n

[1]+  Stopped                 gdb foo

$ fg
gdb foo

Thread 1 "foo" received signal SIGTTIN, Stopped (tty input).
0x5bd015dc in gfortrani_fbuf_read () from /usr/bin/cyggfortran-3.dll

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