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Some people have had there Macs running folding programs 24/7 for long periods of time with no problems. Those things consume 100% CPU all the time. The fans SCREAM!
 
Leave it on if ya want. No harm to them. Infact the less your hard drive has to power up the less strain on it I think? Plus don't worry about heat. The fans control that and it will be sitting on a desk I presume?
 
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