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I need to have one Pi placed on top of the building with an IP camera connected, taking images for a time-lapse video.

For this application, a headless operating system would be enough because bare image taking is done by single command. However everything else like configuring and image management would be easier with graphical environment like Xfce, for example. But I don't want to have a desktop running when I don't need it, because, I am guessing, the CPU and GPU would work more thus temperature of device would be higher.

So how could I do this? Is there an easy way to start a desktop when I needed and by default to have it turned off? Which operating system would you recommend?

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    a running but unused desktop will have a very small effect on temperature, I think you are prematurely optimizing. I would be more worried about the temperature on the roof rather than the temp of the Pi. If you insist on doing this you could start your Pi with the command line as default then type startx to start a graphical session. – Steve Robillard Jun 16 '17 at 10:42
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What GUI's are fundamentally greedy about is memory; if you have enough free, using one won't hurt the performance of other applications.

There is a hopefully obvious caveat to that: If you run very active graphical apps, they may require a lot of processor time. One way to judge this is whether they are actually doing something besides sitting around. For example, a web browser may hog processor time if you have pages loaded with javascript animations which run incessantly.

A more definitive way is to run a process monitor such as top or htop. I believe by default these rank by CPU time. Generally they use a little bit themselves, which you will notice if you run one on a fairly idle system; the monitor process itself will be near the top, consuming 1-2%. You can diminish that by configuring them to sample less often; once or twice a second should be fine on a pi and still fulfill the purpose.

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