When a thread executing user code is waiting for input, how does the scheduler know to interrupt it or how does the thread know to call the scheduler, seeing as the average programmer of a simple single threaded application is unlikely to insert sched_yield() everywhere. Does the compiler insert sched_yield() on optimisation or does the thread just spin lock until the general timer interrupt set by the scheduler fires, or does the user have to explicitly state wait(), sleep() functions in order for the context to switch?
This question is especially relevant if the scheduler is not preemptive because then it has to call the scheduler when it is waiting for input for throughput to be effective, but I'm not sure how it does this.
Be careful not to confuse preemption with the ability of a process to sleep. Processes can sleep even with a non-preempting scheduler. This is what happens when a process is waiting for I/O. The process makes a system call such as read() and the device determines no data is available. It then internally puts the process to sleep by updating a data structure used by the scheduler. The scheduler then executes other processes until an interrupt or some other event occurs that wakes the original process. The awoken process then becomes eligible again for scheduling.
On the other hand preemption is the ability of an architecture's scheduler to stop execution of a process without its cooperation. The interruption can occur anywhere in the program's instruction stream. Control returns to the scheduler which can then execute other processes and return to the interrupted (preempted) process later. Most schedulers allocate time slices where a process is allowed to run for up to a predetermined amount of time, after which it is preempted if higher-priority processes need time slices.
Unless you're writing drivers or kernel code, you don't need to worry about the underlying mechanisms too much. When writing user-space applications the key concepts are (1) that some system calls may block which means your process is put to sleep until an event occurs, and (2) on preemptible systems (all mainstream modern operating systems) your program may be preempted at any time so that other processes can run.
* Note that in some platforms, such as Linux, a thread is really just another process which shares its virtual address space with another process. Processes and threads are therefore treated exactly the same by the scheduler.