Modern chips (pentium 4 and later) have counters inside of them that could be used to calculate this...for a range of time, and using the proper tools.
There are many monitoring counters inside of modern CPUs that count all kinds of esoteric things. # of floating point instructions that are "retired", # of times cache misses occured (ie memory was directly read from), and so on.
There are programmer tools from both Intel and AMD that can be used to setup these timers, run a program for a specified length of time, and then read these counters.
I guess the most important thing to really do would be to specify when to start counting: the beginning of seti run of a full WU?, only for a section (function) of the seti code?
and for how long: Full WU run?, after WU is read from data file into RAM?
and under what conditions: Only for certain angle ranges?