CPU Cycle count based profiling in C/C++ Linux x86_64

You are on the right track¹, but you need to do two things:

1. Run cpuid instruction before rdtsc to flush the CPU pipeline (makes measurement more reliable). As far as I recall it clobbers registers from eax to edx.
2. Measure real time. There is a lot more to execution time, than just CPU cycles (locking contention, context switches and other overhead you don't control). Calibrate TSC ticks with real time. You can do it in a simple loop that takes differences in measurements of, say, gettimeofday (Linux, since you didn't mentioned the platform) calls and rdtsc output. Then you can tell how much time each TSC tick takes. Another consideration is synchronization of TSC across CPUs, because each core may have its own counter. In Linux you can see it in /proc/cpuinfo, your CPU should have a constant_tsc flag. Most newer Intel CPUs I've seen have this flag.

¹I have personally found rdtsc to be more accurate than system calls like gettimeofday() for fine-grained measurements.

I personally think the rdtsc instruction is great and usable for a variety of tasks. I do not think that using cpuid is necessary to prepare for rdtsc. Here is how I reason around rdtsc:

1. Since I use the Watcom compiler I've implemented rdtsc using "#pragma aux" which means that the C compiler will generate the instruction inline, expect the result in edx:eax and also inform its optimizer that the contents of eax and edx have been modified. This is a huge improvement from traditional _asm implementations where the optimizer would stay away from optimizing in _asm's vicinity. I've also implemented a divide_U8_by_U4 using "#pragma aux" so that I won't need to call a lib function when I convert clock_cycles to us or ms.
2. Every execution of rdtsc will result in some overhead (A LOT more if it is encapsulated as in the author's example) which must be taken more into account the shorter the sequence to measure is. Generally I don't time shorter sequences than 1/30 of the internal clock frequency which usually works out to 1/10^8 seconds (3 GHZ internal clock). I use such measurements as indications, not fact. Knowing this I can leave out cpuid. The more times I measure, the closer to fact I will get.
3. To measure reliably I would use the 1/100 - 1/300 range i/e 0.03 - 0.1 us. In this range the additional accuracy of using cpuid is practically insignificant. I use this range for short sequence timing. This is my "non-standard" unit since it is dependent on the CPU's internal clock frequency. For example on a 1 GHz machine I would not use 0.03 us because that would put me outside the 1/100 limit and my readings would become indications. Here I would use 0.1 us as the shortest time measurement unit. 1/300 would not be used since it would be too close to 1 us (see below) to make any significant difference.
4. For even longer processing sequences I divide the difference between two rdtsc reading with say 3000 (for 3 GHz) and will convert the elapsed clock cycles to us. Actually I use (diff+1500)/3000 where 1500 is half of 3000. For I/O waits I use milliseconds => (diff+1500000)/3000000. These are my "standard" units. I very seldom use seconds.
5. Sometimes I get unexpectedly slow results and then I must ask myself: is this due to an interrupt or to the code? I measure a few more times to see if it was, indeed, an interrupt. In that case ... well interrupts happen all the time in the real world. If my sequence is short then there is a good possibility that the next measurement won't be interrupted. If the sequence is longer interrupts will occur more often and there isn't much I can do about it.
6. Measuring long elapsed times very accurately (hour and longer ETs in us or lower) will increase the risk of getting a division exception in divide_U8_by_U4, so I think through when to use us and when to use ms.
7. I also have code for basic statistics. Using this I log min and max values and I can calculate mean and standard deviation. This code is non-trivial so its own ET must be subtracted from the measured ETs.
8. If the compiler is doing extensive optimizations and your readings are stored in local variables the compiler may determine ("correctly") that the code can be omitted. One way to avoid this is to store the results in public (non-static, non-stack-based) variables.
9. Programs running in real-world conditions should be measured in real-world conditions, there's no way around that.

As to the question of time stamp counter being accurate I would say that assuming the tsc on different cores are synchronized (which is the norm) there is the problem of CPU throttling during periods of low activity to reduce energy consumption. It is always possible to inhibit the functionality when testing. If you're executing an instruction at 1 GHz or at 10 Mhz on the same processor the elapsed cycle count will be the same even though the former completed in 1% of the time compred to the latter.

Trying to count the cycles of an individual execution of a function is not really the right way to go. The fact that your process can be interrupted at any time, along with delays caused by cache misses and branch mispredictions means that there can be considerable deviation in the number of cycles taken from call to call.

The right way is either:

• Count the number of cycles or CPU time (with clock()) taken for a large number of calls to the function, then average them; or
• Use a cycle-level emulating profiler like Callgrind / kcachegrind.

By the way, you need to execute a serialising instruction before RDTSC. Typically CPUID is used.