Profiling comes in three different flaviors. The first is emulation, where a processor behavior is emulated, the second is sampling, where at regular intervals, the profiler samples the status of a program, and fianlly instrulentation, where the profiler gets information when a subroutine is called and when it returns. As with the Heisenberg uncertainty, profiling changes the exact behavior of your program. This is something you have to remember when analyzing a profile.
Valgrind is an Open Source emulation profiler. It is freely available on standard Linux platforms. As it is an emulation, it is far slower than the actual program. This means that the I/O are underestimated. The advantage is that you can have every detail on the memory behavior (cache misses for instance). Valgrind does not emulate all processors, but you can tweak it to approach your own one.