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While trying to set up partition from Arch Linux installation CD(using cfdisk) itself the following error showed up-

Bad primary partition 2: partition ends in final partial cylinder

How do I fix it?

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    I think it means that your disk does not consist of an integer number of cylinders. Some tools and OSes like partitions to consist of an integer number of cylinders (typically 1cyl is a few MB), but the boundaries are stored with sectors (always 512B until recently) as the unit, and Linux doesn't require any alignment. – Gilles Jan 7 '11 at 18:32
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  1. Fetch sysresccd (skip step if the you don't need any kind of GUI and parted is on arch disk). It is usefult to have a copy anyway.
  2. Use gparted/parted to partition harddrive (the latter is present IIRC)
  3. Resume installing

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