Difference between CLOCK_REALTIME and CLOCK_MONOTONIC?

CLOCK_REALTIME is affected by NTP, and can move forwards and backwards. CLOCK_MONOTONIC is not, and advances at one tick per tick.

Robert Love's book LINUX System Programming 2nd Edition, specifically addresses your question at the beginning of Chapter 11, pg 363:

The important aspect of a monotonic time source is NOT the current value, but the guarantee that the time source is strictly linearly increasing, and thus useful for calculating the difference in time between two samplings

That said, I believe he is assuming the processes are running on the same instance of an OS, so you might want to have a periodic calibration running to be able to estimate drift.

CLOCK_REALTIME represents the machine's best-guess as to the current wall-clock, time-of-day time. As Ignacio and MarkR say, this means that CLOCK_REALTIME can jump forwards and backwards as the system time-of-day clock is changed, including by NTP.

CLOCK_MONOTONIC represents the absolute elapsed wall-clock time since some arbitrary, fixed point in the past. It isn't affected by changes in the system time-of-day clock.

If you want to compute the elapsed time between two events observed on the one machine without an intervening reboot, CLOCK_MONOTONIC is the best option.

Note that on Linux, CLOCK_MONOTONIC does not measure time spent in suspend, although by the POSIX definition it should. You can use the Linux-specific CLOCK_BOOTTIME for a monotonic clock that keeps running during suspend.

POSIX 7 quotes

POSIX 7 specifies both at http://pubs.opengroup.org/onlinepubs/9699919799/functions/clock_getres.html:

CLOCK_REALTIME:

This clock represents the clock measuring real time for the system. For this clock, the values returned by clock_gettime() and specified by clock_settime() represent the amount of time (in seconds and nanoseconds) since the Epoch.

CLOCK_MONOTONIC (optional feature):

For this clock, the value returned by clock_gettime() represents the amount of time (in seconds and nanoseconds) since an unspecified point in the past (for example, system start-up time, or the Epoch). This point does not change after system start-up time. The value of the CLOCK_MONOTONIC clock cannot be set via clock_settime().

clock_settime() gives an important hint: POSIX systems are able to arbitrarily change CLOCK_REALITME with it, so don't rely on it flowing neither continuously nor forward. NTP could be implemented using clock_settime(), and could only affect CLOCK_REALTIME.

The Linux kernel implementation seems to take boot time as the epoch for CLOCK_MONOTONIC: Starting point for CLOCK_MONOTONIC