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Am I right thinking that UEFI and GPT completely deprecate all the CHS/MBR legacy and eliminate all the sector size related problems (alignment, max drive size, etc.) as well as partitioning limitations (like the maximum of 4 primary partitions)?

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It was my understand that GPT had a maximum of 4 partitions. UEFI doesn't look to address any of the problems you describe. Besides most motherboards on the market for the last 3 years have had UEFI. –  Ramhound Jun 22 '12 at 11:14
    
@Ramhound: GPT supports up to 64 partitions. –  jlliagre Jun 22 '12 at 12:31
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The default partition table size in GPT is 128, not 64. That limit is not a constant, though; it can be adjusted by partitioning software that supports this change, such as GPT fdisk (gdisk). There is a minimum size for the data structures that works out to 128 partitions, so if you follow the spec, the partition table size can only be increased; but as a practical matter, smaller partition table sizes also work. –  Rod Smith Aug 31 '13 at 17:21

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It makes some limitations large enough for them not to be a problem anymore (eg: 64 partitions vs 4, maximum partition/disk size several zettabytes) but as far as I know, GPT doesn't address the sector size issue.

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Am I right that in case I partition my hard drive with GPT, I don't have to bother about huge drives' sector alignment even if the drive frmware doesn't address this problem itself (like Seagate's consumer models do)? –  Ivan Dec 26 '12 at 20:02
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Have a look to this question: superuser.com/questions/297232/is-gpt-aligned-for-4k-blocks –  jlliagre Dec 26 '12 at 22:06

Let's cover each of the issues in turn:

  • CHS -- GPT uses logical/linear block addressing (LBA) exclusively, so CHS geometry issues go away when using GPT. (There are CHS values in the GPT's protective MBR, but that's there only to keep GPT-unaware tools from messing with the disk. Although the GPT spec is quite explicit about what should go in the protective MBR's CHS fields, many tools seem to play "fast and loose" with this, and most OSes don't seem to care what's in them.) Note that even MBR doesn't really use CHS any more. Although CHS values are part of the MBR data structures, they top out at about 8GB, which is puny by today's standards. Instead, modern disks use 32-bit LBA values to define partitions; the CHS values are ignored for most purposes and on most disks.
  • Alignment -- Because GPT uses LBA and ignores CHS, partition alignment to cylinder values becomes irrelevant with GPT. There are, however, new alignment requirements with Advanced Format disks, some types of RAID arrays, and SSDs. These requirements apply to both GPT and MBR disks, and they make it desirable to align partitions on certain power-of-2 multiples of sector numbers. Modern partitioning tools therefore align partitions on 2048-sector (1MiB) boundaries by default, which works well with most disks. (Some SSDs require even higher alignment values, though.) This alignment issue is one that relates to the disk hardware, not to the partitioning system, so you should consult the hardware manufacturer if you're in doubt about partition alignment for a specific device.
  • Maximum drive size -- MBR uses 32-bit LBA values. Combined with a 512-byte sector size, this works out to a maximum of 2TiB. GPT uses 64-bit LBA values, which works out to a disk-size limit of 8ZiB. Both of these limits go up if the sector size also goes up. Some disks today (mostly external models) use 4096-byte sectors, for limits of 16TiB on MBR or 64ZiB on GPT.
  • 4-partition limit -- GPT uses a partition table that holds 128 partitions by default, but this value can be raised if necessary. GPT fdisk (gdisk) can do this, for instance. GPT has no need for extended or logical partitions, and in their absence, it doesn't really make sense to refer to GPT's partitions as "primary," although that is sometimes done, particularly by partitioning software that handles both partition table types.
  • Sector size -- Both MBR and GPT work fine on disks with sectors that have sizes other than 512 bytes. This has been true for years, in fact; a decade ago I used magneto-optical (MO) disks with 2048-byte sectors with MBR. Some parts of the software stack, though, including at least some BIOSes, have hard-coded assumptions of 512-byte disks, so booting from such a disk might be a problem with some BIOSes. I don't know how widespread such problems are. EFI supposedly eliminates such assumptions in the firmware, but I've not tested this myself.

Note that most of these issues relate to the differences between MBR and GPT. GPT can be used even on BIOS-based computers, although Windows refuses to boot from a GPT disk on such a computer. The only one of these issues that's directly related to BIOS vs. EFI is in their support for booting from disks with other-than-512-byte sectors.

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