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I know that you can only have 4 primary partitions on a hard drive. But if you're using less than 4, is there a benefit/penalty for using logical partitions?

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The limit of 4 partitions is valid only in MBR partition scheme. There is no such limit with GPT (see en.wikipedia.org/wiki/GUID_Partition_Table) –  mouviciel Sep 30 '10 at 11:05
@mouviciel: Good point –  Falmarri Sep 30 '10 at 18:37
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2 Answers

Today, it doesn't really matter if you use primary or extended partitions.

There have been times where /boot had to be a primary partition but this isn't true any more. Also earlier incarnations of MS Windows required that you installed Windows to a primary partition.

When I set up a new disk, I make the first partition primary and put /boot there and put the rest as logical partitions into one big extended but this is just a personal preference.

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I would say that there is indeed some penalty if you use logical instead of primary partitions:

  1. Primary Partitions reside on the first sector - that is a well known place - as opposed to an extended partition.
  2. AFAIK BIOS will still only boot from an active primary partition - so you have the choice to put any bootloader on any of those partitons and make it active.

So if you have up to 3 partitions keep them primary. If you have 4 or more, use the 4th as extended partition and start using logicals.

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Some badly behaved bioses check that a primary partition is marked active, or they refuse to boot. Otherwise, they just load and execute the boot loader in the MBR, most of which are perfectly capable of booting from a logical partition these days. –  psusi Oct 1 '11 at 1:01
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