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So I installed Ubuntu 12.04 and now my case fans never run, even when booted into Windows 7. The only fans that ever come on are fans directly attached to a device (i.e. cpu/gpu/psu). Anything on a molex connector never spins up. Has anyone seen this? I've tried reseting my bios to defaults but that didn't do anything. I guess grub is the only common denominator between Linux/Windows? My case fans used to come on the second I hit the power on, though, which is pre grub.

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This is surely a hardware problem. Even grub is not read until the disk is accessed. Check fuses, connectors, etc. – Marty Fried Jul 31 '12 at 23:14
up vote 1 down vote accepted

If you're using fans powered by the 4-pin molex connectors, and they aren't coming on at all, then there is a problem with your power supply I would suspect, or the fans themselves. In fact, I would be surprised for you to have anything powering on at that point.

It is a hardware issue, unrelated to Ubuntu.

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haha wow, I feel like an idiot :p Apparently I was doing something in the case around the same time I installed Ubuntu. I opened it up and the Molex cable was joggled loose. Plugged it back in and everything is fine. – Andrew Myers Aug 3 '12 at 13:46

Dobey's right. It's probably a hardware issue.

If you don't have any reason to doubt your PSU, try jiggling cables and making sure all the connections are in all the way. Also, make sure the fans are enabled in the BIOS.

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