as per the vSphere 5 Storage Best Practices mentioned in the vmworld 2012 doc INF-STO2980
the storage geeks... says
Alignment is Optimal I/O
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VMware, Microsoft, Citrix, NetApp, EMC all agree, align partitions
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Plug-n-Play Guest Operating Systems
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Windows 2008, Vista, & Win7
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Fresh installations only– no upgrades
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Guest Operating Systems requiring manual alignment
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Windows NT, 2000, 2003, & XP (use diskpart to set to 1MB)
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Linux (use fdisk expert mode and align on 2048 = 1MB)