Problem with pThread sync issue

Question

I am facing a sync issue with pthread. threadWaitFunction1, is a thread wait function. I expect line no. 247 flag = 1 to be executed only after 243-246 has fini

Answer 1

So it is not really execution ordering (which is most probably correct) but timing that makes you unhappy. And under "it jumps directly to 247 before 243-246 has finished" you mean "I observed it executing 247 before the time it should wait in 244 has passed". Right?

Then, I suspect this is the problem of spurious wakeup: a thread might get woken up even though no other thread signalled the condition variable. The specification of pthread_cond_timedwait() says that "Spurious wakeups from the pthread_cond_timedwait() or pthread_cond_wait() functions may occur."

Usually, a condition variable is associated with a certain event in the application, and a thread waiting on a condition variable in fact waits for a signal by another thread that the event of interest has happened. If you have no event and just want to wait for a certain amount of time, indeed other ways, such as usleep() or timers, are more appropriate, except if you also need a pthread cancellation point.

ADDED: Since you seem satisfied with usleep() and only asked why pthread_cond_timedwait() did not work to your expectations, I decided not to post the code. If you need it, you may use the answer of @Hasturkun.

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ADDED-2: The output in comments below (obtained after the solution of Hasturkun was applied) suggests that the waiting thread does not exit the loop, which likely means that pthread_cond_timedwait() returns something different than ETIMEDOUT. Have you seen the comment by @nos to your post (I fixed the amount of nanosecs to subtract):

Make sure (now.tv_usec * 1000) + lt_leak_start_nsec; doesn't overflow. You can only set tv_nsec to max 999999999, if the expression is larger than that, you should subtract 1000000000 from tv_nsec, and increment tv_sec by 1. If your timeToWaitPtr contains an invalid tv_nsec (larger than 999999999), pthread_cond_timedwait will fail (you should check its return value too.) – nos Apr 28 at 19:04

In this case, pthread_cond_timedwait() will repeatedly return EINVAL and will never get out of the loop. It is better to adjust the timeout before entering the wait loop, though it can also be done in response to EINVAL.

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ADDED-3: Now after you changed the code in your question to pass the timeout without adding to current time, it has another problem. As stated in the spec, the timeout for pthread_cond_timedwait() is absolute time, not relative; so when you pass something like 3 sec as the timeout, it is interpreted as "3 seconds since the reference point for the system time". That moment is almost certainly passed for a while, and so pthread_cond_timedwait() returns immediately.
I would recommend you to read the specification thoroughly (including rationale) to build better understanding of how this function is supposed to be used.