Accurate timing in C code

What can I use for accurately measuring elapsed time in C code? I'm
looking for round about millisecond accuracy. I've written some code to
wait for vsyncs using OpenGL, but while glXGetRefreshRateSGI reports a
consistent 59Hz, measuring the time between two syncs with gettimeofday
results in a period corresponding to anything up to 88Hz, although it
does seem to usually give 59.8802.

I tried clock(), but that doesn't return anything useful.

Most video players seem to use /dev/rtc but I can't find useful
documentation about it. The kernel docs suggest that the way it's used
is that you program it with the frequency you want it to generate
interrupts (requiring root access for >64Hz, so that's a problem for a
start). Wouldn't that affect the whole machine? What if two applications
want to use it at the same time, at different frequencies? And the clock
can be disturbed by its being kept in sync with external sources etc.

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