what happens when we set different processor affinity to process and its thread in linux.
I am trying to start a process affined to a core (say 1) which have two threads one of which need to run on other core (say 0)
When i tried to set affinity to thread different to process the program got executed. but I want to know the hidden impacts of this approach.
Threads and processes are vastly the same thing. Whether you call pthread_setaffinity... or use the sched_setaffinity syscall, they both affect the current thread's affinity mask. This may be your "process" thread, or a thread you created.
However, note that a new thread created by pthread_create inherits a copy of its creator's CPU affinity mask [1].
That means that setting the affinity and creating a thread is not the same as creating a thread and setting the affinity. In the first case, both threads will compete over the same processor (which is most probably not what you want) and in the second case they will be bound to different processors.
Also note that while binding threads to a dedicated processor (core) may have advantages in some situations, it may just as well be a very stupid thing to do. Playing with the affinity mask means you limit the scheduler in what it can do to make your program run. If the core you bound your thread to isn't available, your thread will not run, end of story.
This is a very similar reasoning/strategy as disabling swap to make the system "faster" (some users still do that!). By doing so they usually gain nothing, all they do is limit what the memory manager can do by removing one option of providing a free page once it runs out of unused physical RAM. Usually this means something more or less valuable from the buffer cache is purged when instead some private page that wasn't used in hours could have been swapped out.
Usually people use affinity because they have this idea that the scheduler will make threads bounce between processor cores all the time and this is bad. Processor migration indeed is not cheap, but the scheduler has a mechanism which makes sure it does not happen before a certain minimum amount of time (there is a /proc thingie for that too). After a longer amount of time, all advantages of staying at the old core (TLB, cache) are usually gone anyway, so running on a different core which is readily available is actually better than waiting for a particular core to maybe, eventually become available.
NUMA architectures may be a different topic, but I'd assume (though I don't know for sure) that the scheduler is smart enough not to silently migrate a thread to a different node. In general, however, I'd recommend not to play with affinity at all.