VMware Solutions Discussions

Disk alignment for boot-from-SAN Windows 2003 servers


We are have several servers that boot from SAN, using FC LUNs provisioned form a NetApp filer. We are installing Windows 2003 R2 on the LUNs.

How can I ensure that the partition is aligned correctly?


- how can I create an aligned partition for new Windows 2003 installation?

- what to do about physical server already installed on an unaligned partition?

I tried creating the LUN using SnapDrive on another server, then presenting the LUN to the new server. Windows installation refuses to use the partition because it is GPT.

Can anyone post instructions on how to manually create an aligned Windows partition (without the use of SnapDrive)?




1. For virtual machines:

I had this issue on VMWare environment. I did use the mbrscan and the mbralign to align the boot partition. You can find them on the Netapp Host Utilities Tool.

Check the link for it:


2. For physical machines:

I see one option for physical machines, dont know if its going to help you but here it goes.

2.1 First lets start with a non-boot partition alignment:

You can use diskpart to align the partition.

check the link:


*if its an old partition you need to map a new LUN to the server, create a new one aligned and move data.

You can use the diskpart to check if the partition is aligned.

2.2 Now for one boot partition:

1 - Map a new LUN/Share on your filer to you physical server.

2 - Create one aligned partition using diskpart. http://support.microsoft.com/kb/929491

3 - Use any backup solution for backing up your old partition and restore to the new one. could even be the ntbackup

4 - Change boot.ini.

5 - Reboot your server.

6 - Change you HBA boot config, point to the new LUN.

7 - Unmap your old LUN at your filer.

Check this link:


Note: Windows 2008 creates the boot partition aligned. 

Or you can use some partition tool, ^^.

Hope this information can be useful.


I tried creating a partition using diskpart as per information in http://support.microsoft.com/kb/929491. Unfortunately, read/writes are still reported as unaligned.



First you need create vol and Lun for Windows (no GPT).

On Windows system in FC card  setup menu your need create settings for boot to SAN.

On FC switch you need create zone for windows server.

Create initiator group and add to Lun.

Thanks for the basic instructions on how to create a volume and LUN. This is not quite what I need to know...

If I proceed with Windows 2003 installation on the new LUN, the partition will be unaligned.

My question is: how can I install Windows 2003 and ensure that the partition is aligned?

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