I am trying to profile a c++ function using gprof, I am intrested in the %time taken. I did more than one run and for some reason I got a large difference in the results. I
I recommend printing a copy of the gprof paper and reading it carefully.
According to the paper, here's how gprof measures time. It samples the PC, and it counts how many samples land in each routine. Multiplied by the time between samples, that is each routine's total self time.
It also records in a table, by call site, how many times routine A calls routine B, assuming routine B is instrumented by the -pg option. By summing those up, it can tell how many times routine B was called.
Starting from the bottom of the call tree (where total time = self time), it assumes the average time per call of each routine is its total time divided by the number of calls.
Then it works back up to each caller of those routines. The time of each routine is its average self time plus the average number of calls to each subordinate routine times the average time of the subordinate routine.
You can see, even if recursions (cycles in the call graph) are not present, how this is fraught with possibilities for errors, such as assumptions about average times and average numbers of calls, and assumptions about subroutines being instrumented, which the authors point out. If there are recursions, they basically say "forget it".
All of this technology, even if it weren't problematic, begs the question - What is it's purpose? Usually, the purpose is "find bottlenecks". According to the paper, it can help people evaluate alternative implementations. That's not finding bottlenecks. They do recommend looking at routines that seem to be called a lot of times, or that have high average times. Certainly routines with low average cumulative time should be ignored, but that doesn't localize the problem very much. And, it completely ignores I/O, as if all I/O that is done is unquestionably necessary.
So, to try to answer your question, try Zoom, for one, and don't expect to eliminate statistical noise in measurements.
gprof is a venerable tool, simple and rugged, but the problems it had in the beginning are still there, and far better tools have come along in the intervening decades. Here's a list of the issues.
gprof is not very accurate, particularly for small functions, see http://www.cs.utah.edu/dept/old/texinfo/as/gprof.html#SEC11
If this is Linux then I recommend a profiler that doesn't require the code to be instrumented, e.g. Zoom - you can get a free 30 day evaluation license, after that it costs money.
All sampling profilers suffer form statistical inaccuracies - if the error is too large then you need to sample for longer and/or with a smaller sampling interval.