This is a copy of my answer from: C++ Timer function to provide time in nano seconds
For Linux (and BSD) you want to use clock_gettime().
#include <sys/time.h>
int main()
{
timespec ts;
// clock_gettime(CLOCK_MONOTONIC, &ts); // Works on FreeBSD
clock_gettime(CLOCK_REALTIME, &ts); // Works on Linux
}
For windows you want to use the QueryPerformanceCounter. And here is more on QPC
Apparently there is a known issue with QPC on some chipsets, so you may want to make sure you do not have those chipset. Additionally some dual core AMDs may also cause a problem. See the second post by sebbbi, where he states:
QueryPerformanceCounter() and
QueryPerformanceFrequency() offer a
bit better resolution, but have
different issues. For example in
Windows XP, all AMD Athlon X2 dual
core CPUs return the PC of either of
the cores "randomly" (the PC sometimes
jumps a bit backwards), unless you
specially install AMD dual core driver
package to fix the issue. We haven't
noticed any other dual+ core CPUs
having similar issues (p4 dual, p4 ht,
core2 dual, core2 quad, phenom quad).