Aligning Windows Partitions Without Losing Data

First you should probably decide if you want to align all your volumes, or just the data volumes.  Realigning the data volumes can be easily accomplished with tools like Ghost or Clonezilla, or even simply xcopy, robocopy, or backup/restore procedures.  Simply add a new disk, create an aligned partition, and copy the data with your tool of choice.  Doing the same on the boot partition is a little more inovled since it's pretty easy to break the boot loader by moving data all around.

There are several reasons you might want to align your existing boot partition though, in many cases your swap file is on that partition and if your system does any swapping an aligned partition can be much faster.  In our case we had several systems that had been migrated from older systems where everything was all on the C: drive.  These systems used postgres database, did lots of logging, had some MSSQL Express thrown in, etc.  While it might have been possible to reinstall and move all of these applications to a D: drive, it seemed like a lot of work and the documentation on the various apps was pretty weak.  We decided it would be better if we could figure out a way to align the partition data without a reinstall.

This turned out to be much more difficult that I first thought.  We didn't own a version of Ghost that would clone Windows 2003 reliably, and so I went searching for a free solution.  Clonezilla seemed promising, and we created the first clone of our system with it, but we were never able to get the newly cloned, properly aligned partition to boot.

Then I decided to give Gparted a try.  Gparted is a great tool that can boot from a live CD and resize and move your existing partitions.  The thought here was to use Gparted to simply resize the existing partition by 64 sectors and the move it slightly to the right to an aligned location.  Unfortunately Gparted wasn't quite as easy as I had hoped, mainly because the GUI only allows you to set sizes by MiB, not by sector.  Still, I was undeterred, and I found a way to manipulate Gparted to do what I wanted.  It takes two passes, which can take a long time if you have largish system paritions, but most of our were less that 16GB, with typically only about 8GB used.  Here what I did:

!!! MAKE A BACKUP/SNAPSHOT IN CASE THINGS GO WRONG !!!

1.  Make sure the disk is defragmented
2.  Boot the system with the Gparted live CD.
3.  Select the parition you are wanting to resize and choose (Move/Resize)
4.  Shrink the volume by some amount, the smaller you shrink it the faster it will copy during the move step.  I usually shrink it a GB or so larger than the amount of data on the drive.
5.  Move the partition to right by a few MB's to free up space at the start of the disk.
6.  Once the move completes, exit Gparted, not the entire live CD, just the Gparted application
7.  Start the terminal window on the live CD
8.  In the command window type 'parted /dev/sda' (substitute your actual device here) to start the command line parted editor
9.  Create a new partition at the start of the disk to fill in the space up to the section where you want to align your parition.  For example, if you want your system partition to start at sector 128, create a very small partition that takes up space from sectors 63-127.  The command would be something like this:

mkpart primary 63s 127s

This tells parted to create a new primary partition from sector 63 to sector 127.  That means the very next sector available is 128, a stripe aligned partition.  You may want a different start sector based on your array (some use 64K, some 128K, some bigger) but I've found the 128K alignment to work well with both 64K (Equallogic) and 128K (EMC Clariiion) stripe sizes.

10.  Exit parted and restart the Gparted GUI by clicking the Gparted icon.
11.  Use the Move/Resize option to resize the NTFS partition to fill the entire remaining space.  As pointed out by several users, you MUST uncheck the "Round to Cylinders" option prior to this.  I guess I thought this was obvious since we're trying to align to a specific sector but that's why I'm not a documentation writer.
12.  Exit gparted, run parted again, remove the small partition you created earlier and reboot.

Now you have a nice, stripe aligned NTFS partition that should still boot right up normally.  The first reboot will run a checkdisk to make sure all the moving and resizing didn't damage anything on the disk.  Enjoy the improved performance and lowered IOPS on your SAN storage!

Obviously the steps above are just an outline, you really shouldn't try this unless you understand what the above means, but if your comfortable with manipulating partitions the above should be enough to give you an idea what to do.  I've found that the above procedure takes about 15-30 minutes for a typical 8-10GB system partition, so keep that in mind when planning downtime.  Also, make sure your future OS deployments are aligned so you don't have to repeat this again.

The above procedures work for virtual machine too (assuming the VMFS volume is aligned as well, which is done automatically with VI3 volumes and above).  There are some other tools which will to this at the VMDK layer (Netapp has mbralign available to their customers and Vizioncore's vOptimizer Pro will do it without having to copy the entire VMDK) but I don't have any experience with these tools and I needed something that would work for physical machines too.  The above procedure did the trick for me.