Compare Energy Consumption for different phases of a system

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aviian
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I wish to compare energy consumption of my protocol, in embedded systems, in two different phases.
The point is that one phase lasts longer than other (around 130 seconds more). => The longer phase will, of-course, have larger energy consumption since time is a higher quantity in this case.
Can I still compare the overall energy consumption ? or Should i compare instantaneous energy or Power only?
 
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It depends. The average over both phases is useful for dimensioning power supply capacity and (if necessary) the cooling system for the electronics. The peak power tells you something about the need for power decoupling capacitors (and possibly some inductance to limit the peak current).