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I just got a new 1 TB hard drive (WD10EARS) and it says if I want to use more than 1 large partition I must download the Acronis WD Align software to "align" the partitions. I tried just creating the partitions the usual old way, but my computer seems to have problems writing to the drive. So I'm in the middle of the alignment process, which it says will take 14 (scracth that, it's now 15) hours to complete. So, what is it actually doing, and will the "alignment" fix my write issues?

Update:

I was actually doing 2 drives, which I am going to use as a mirrored RAID. After 15 hours, the process did complete successfully. It seems extremely long, but it did work out in the end. All my performance problems were gone. Anyway, I just wanted to ensure that everything was working before I set up the RAID. After reinstalling Windows now with RAID on the 2 drives, I was able to partition the RAID device as I normally would, as the drive was not exposed directly to the OS.

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3 Answers

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You have as so-called "512e" disc. Your disc unit operates internally in terms of 4KiB sectors, but your system software is seeing a disc that operates in terms of 0.5KiB sectors as discs have heretofore done. Partition alignment to 4KiB/1MiB multiples helps to combat the eightfold or more performance penalty that 4KiB physical sectors involves. If you used a Microsoft disc partitioning tool (other than diskpart) from before 2008, or even a modern Linux fdisk, it won't have aligned the partitions to 4KiB multiples, and you'll suffer the performance penalty.

Realignment is lengthy, but not that lengthy. (Realigning a ~1TiB partition involves reading and rewriting ~1TiB of the disc, remember, as the entire partition contents have to be shifted up or down.) You are better off starting by partitioning your disc afresh, with the correct partition alignment, give that you are, here, starting from a blank disc anyway

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It is enabling the hard drive to read and write more data into the same available space on the hard drive.
I'm guessing you're using Windows XP as the drives are automatically optimised for Windows Vista 7 and OSx Tiger and above.
The 15 hours seems a long time. WD reckon it should take about 20minutes on a new drive.
You may want to look here for more information

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I'm submitting a ticket to Western Digital about it. 15 hours does seem excessively long. –  Kibbee Sep 3 '11 at 11:52
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The Partitioning advice page from Gdisk documentation explains why alignment is needed.

The standard sector size for hard disks used to be 512 bytes. This was okay in the beginning, but as disk density increases the small sectors cause various defects, so most manufacturers now use 4096 byte sectors for their "Advanced Format" disks. However, not all operating systems can work with 4096-byte sectors (Windows cannot), so by default such disks use a "512 emulation" (512e) mode, in which a single long sector is presented to the OS as four 512-byte sectors.

On a higher level, most filesystems also allocate disk space in clusters or blocks – very often of 4096 or 8192 bytes in size. If partitioning is done while disk is in 512e mode, older partitioning programs would align partitions to the smaller sector size – or even to cylinder length, even though cylinder addressing is very much obsolete. (Newer tools align to 1 MiB boundaries.)

With 512-byte sectors this is not a problem. A single cluster is written to eight sectors, and if only a few bytes are changed, then only one sector has to be rewritten.

file sys:      | ' ' ' ' ' ' ' | ' ' ' ' ' ' ' | ' ' ' ' ' ' ' |
hard disk: | | | | | | | | | | | | | | | | | | | | | | | | | | | | |...

If the disk uses 4096-byte sectors, however, and the partition was cylinder-aligned, it would often end up starting in the middle of a physical 4096-bit sector:

file sys:      | ' ' ' ' ' ' ' | ' ' ' ' ' ' ' | ' ' ' ' ' ' ' |
hard disk: | ' ' ' ' ' ' ' | ' ' ' ' ' ' ' | ' ' ' ' ' ' ' | ' ' ' ' ' ' ' |

Disks can only read or write a whole sector at once, so updating a single filesystem cluster would, in this situation, require the disk to read and write twice as much as necessary, resulting in (often serious) performance issues. Even if a filesystem cluster is only written to, the disk still has to read both sectors, and only update the affected part.

The "realignment" program likely just shifts the filesystem to have filesystem clusters aligned with disk sectors.

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"as disk density increases the small sectors cause various defects" – I don't understand how a relative size can cause a defect. Please, can you clarify, or provide a link? –  Graham Perrin Sep 16 '12 at 18:14
    
@GrahamPerrin: (To be honest, I don't even remember writing that...) The sentence is probably from the software perspective – the smaller (in bytes) sectors are, the more sectors a disk has; and there can be limits on how many sectors can be addressed by various systems. For example, the "MBR" partition table uses 32 bits for sector addresses, so with 512-byte sectors, it can use at most 512 bytes × 2^32 sectors = two terabytes of a disk. (GPT avoids this by using 64 bit addresses, but some systems require MBR.) –  grawity Sep 16 '12 at 18:47
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