[dimfeld]

Usually the debugger just replaces the breakpoint instruction with the original byte, then resumes execution in a single-step mode that causes the CPU to just execute a single instruction before firing another interrupt. After that, the debugger sets the breakpoint again and resumes normal execution.

[to3m]

When single-stepping, it's necessary to step only one thread, to ensure that other threads don't skip the (temporarily) disabled breakpoint. There's a paper here that discusses one solution to the problems this causes: http://www.bmrtech.com/uploadfile/image/whitepaper/mentorpap...

(You can engineer a deadlock in gdb due to this, e.g., on x64, by stepping over a SYSCALL instruction that reads from a pipe that's about to be filled by another thread. But you're unlikely to experience this in practice, as system calls are wrapped by a glibc function, and you'll probably be stepping over that rather than the instruction directly.)