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So this is my first time installing a second OS on a PC. My tower is running Windows 8 64-bit, and I installed Ubuntu 13.04 from USB following the official instructions. My tower has 3 hard drives, a 1TB HDD (with Win8 on it), a 2TB HDD, and a 60GB SSD. When I first tried to install, the Ubuntu installer asked to install on the SSD by default, and I allowed it to. I was then unable to actually boot to the install I had done (putting that drive first in the BIOS boot order did nothing), so I decided to reinstall.

I launched the live USB again and chose to install on my main 1TB drive, alongside Windows. I created a new partition following the top answer on this question (making it an ext4 with mount point "/"), and lo and behold, the installation goes without a hitch. However, now I can't boot at all - I try to start my computer, and when it loads my 1TB drive I get a flashing command prompt bar.

I once again launch live USB and find a guide to reinstalling GRUB (sorry, can't find it right now), which then allows me to see GRUB when I turn my computer on and boot from my 1TB drive. Ubuntu launches correctly, but when I try to launch Windows 8 now, I get a message saying it's preparing automatic repairs, and then attempting repairs. It sits on that screen indefinitely apparently (I left it for 20 minutes with no change).

I really only needed Ubuntu as a clean workspace for phone modding, but Windows 8 is where I kept all my stuff. I'd really, really like to hear that I haven't broken everything. Anyone have advice for me?

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I just found this from windows 8 community, though it will probably mess with your Ubuntu install: answers.microsoft.com/en-us/windows/forum/windows_8-system/…. If you don't need to boot into windows, you should be able to copy all your data from the windows drive. –  DaboRoss Jun 9 '13 at 5:49
    
I know that windows 8 doesn't like having anything else change the hard drive. If it would just not check, there probably wouldn't be a problem. I can't verify this though. –  DaboRoss Jun 9 '13 at 5:54
    
Unfortunately, I do need to boot into Windows still. When they say to do a selective boot through BIOS, what exactly do they mean? I don't see any options for specific partitions, I can only choose different devices. I'm about to go grab my Win8 install disc and see if that allows me t run a boot troubleshooter. –  DavisJ3608 Jun 9 '13 at 6:01
    
I am not sure, just found that link. I would suggest repairing from the install disk, though because I don't have windows 8 I can't guarantee it will work. Also the install disk might mess up your ubuntu install, so make sure to backup any files you have on ubuntu before using it. Probably the thing that windows didn't like is resizing the partition (if you did that). –  DaboRoss Jun 9 '13 at 6:22
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Add more information about your computer hardware. Did it come Windows 8 preinstalled? Did you have "No root file system is defined" error before you followed that guide? Do you know about UEFI and secure boot issues? Did you have hybrid boot turned on in Windows before installing Ubuntu? –  Tanel Mae Jun 9 '13 at 8:03
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