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I am confused about partitioning a hard drive.
Recently I have been trying to install Windows 7 on a new computer, and I noticed that Windows setup will attempt to automatically partition the hard drive while giving you very few options to finetune the partition layout. Additionally, there will be quite some unpartitioned space left on the HDD i.e. the first partition starts on sector 2048 (as opposed to sector 63), there is inter-partition space present between primary partitions, and the HDD ending also has some unpartitioned sectors. Unhappy about this, I decided to use a live Linux CD to manually partition the HDD, and then run the Windows setup on existing partitions.

My question is why are the partitions not packet tightly together? What is the reason that windows setup will leave such gaps (inter-partition space) on the HDD? Is there a benefit for using such segmented partition layout?

Wishing to keep the unpartitioned space to a minimum, are there any drawbacks, if I manually partition the HDD in such a way that the first partition starts on sector 64 (not 63), that there are no gaps (unused sectors) between primary partitions, and that there is no unpartitioned space left at the ending? All given sector numbers are divisible by 8... If 1 sector = 512 bytes, 8 sectors = 4096 bytes. The partition boundaries are divisible by 4096.

Example:

   Device Boot      Start         End      Blocks   Id  System  
/dev/sda1              64   409600063   204800000   83  Linux  
/dev/sda2       409600064   976773167   283586552   83  Linux  

Total sectors: 976773168

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The starting at 1MB (2048 sectors of 512 bytes) makes sense because it aligns with a lot of different setups. (Think RAID, AF drives etc etc). And a megabyte is usually not missed on today multi-terabyte drives. –  Hennes Oct 24 '12 at 18:53
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On the other hand, aligning to cylinders or 63 sectors doesn't help these days anymore – it may even make things worse. –  grawity Oct 24 '12 at 18:56
    
@Cpp: the partitions in your example are packed tightly together. so, you are complaining about the starting offset? sometimes you want some space at the beginning for, lets say, a bootmanager. –  akira Oct 25 '12 at 5:11
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