One limitation has to do with accuracy of timing information. There is a fundamental problem with deterministic profilers involving accuracy. The most obvious restriction is that the underlying ``clock'' is only ticking at a rate (typically) of about .001 seconds. Hence no measurements will be more accurate than the underlying clock. If enough measurements are taken, then the ``error'' will tend to average out. Unfortunately, removing this first error induces a second source of error.
The second problem is that it ``takes a while'' from when an event is dispatched until the profiler's call to get the time actually gets the state of the clock. Similarly, there is a certain lag when exiting the profiler event handler from the time that the clock's value was obtained (and then squirreled away), until the user's code is once again executing. As a result, functions that are called many times, or call many functions, will typically accumulate this error. The error that accumulates in this fashion is typically less than the accuracy of the clock (less than one clock tick), but it can accumulate and become very significant.
The problem is more important with profile than with the lower-overhead cProfile. For this reason, profile provides a means of calibrating itself for a given platform so that this error can be probabilistically (on the average) removed. After the profiler is calibrated, it will be more accurate (in a least square sense), but it will sometimes produce negative numbers (when call counts are exceptionally low, and the gods of probability work against you :-). ) Do not be alarmed by negative numbers in the profile. They should only appear if you have calibrated your profiler, and the results are actually better than without calibration.
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