Shrink a VMware .VMDK virtual disk

Question ID : 205
Created on 2012-04-01 at 2:02 PM
Author : Guru Corner []

Online URL :

Ran into an issue recently with one of my VMs. Wanted to back it up but was 200GB. I knew there wasn’t that much data on it anymore, it had just grown to that. But in Windows when you delete a file you don’t delete it really, Windows just flags it to be overwritten.

You can use this tool first but don’t think it’s needed. CCleaner and Fileshredder can do the same. That is, wipe the free space while in Windows.

SDelete Sysinternals as MS

In Windows go to a CMD and to the location of sdelete and type

sdelete -c

That cleans the free space. Then shut down the VM.

Once shut down go to a CMD and go to where VMWARE is installed. Mine is

D:Program Files (x86)VMwareVMware Workstation

Then run vmware-vdiskmanager.exe to shrink the VM. This is done with the -k switch.

My VM was in a different location to the diskmanager tool so ended up like this

vmware-vdiskmanager.exe -k “f:vmtest labxp.vmdk”

Once you hit enter you should see a Shrink: 0% meaning it’s started. Could take a while. I just left mine running while at work so don’t know how long it took.

The ” are needed it appears.

It works great. Mine went from 200GB to 26GB.


1. Defragment your virtual disk

Use the build-in defrag-tool in Windows or a third part tool of your choice.

2. Shrink the disk using VMware tools inside the virtual machine

Go ahead and open the VMware toolbox and find the “Shrink” function

When you click the “Prepare to shrink” you start a two stage process; first the application fills all vacant space on the harddrive with large empty files

This process will take quite some time if you have a lot of unused space on your disk. If you look at the root of the harddrive, you’ll find that it simply generates a number of 2 gig files named “wiper0″, “wiper1″ etc..

These files are simply used to overwrite any “deleted” files on the disk; when Windows deletes a file, it doesn’t actually remove the data, it just removes any reference to it – therefore it still takes up space on your disk. The “wiper”-files allow ESX to identify truly unused blocks on your disk.

The next step the Toolbox is to supposed to do, is to tell the ESX host to do the Shrink

But unfortunately this is never done. Hence we need to do some additional work:

3. Take a snapshot of the virtual disk

This is done to have a static non-changing disk file to work on. When a snapshot is active, every change to the harddrive is written into a separate delta-file.

4. Open a session to an ESX host with access to the storage

Either use a SSH client or access the service console directly – make sure to be “root” before you try to proceed.

Change directory to where the virtual machines stores its files:

cd /vmfs/volumes/netapp10/Win2003helper/

In this example my storage is named “netapp10″ and the virtual machine is called “Win2003helper”.

A simple “ls -l” command reveals which files exists, the interesting ones are:

-rw-------    1 root     root     16795648 Oct  7 13:15 Win2003helper-000001-delta.vmdk
-rw-------    1 root     root          235 Oct  7 13:14 Win2003helper-000001.vmdk
-rw-------    1 root     root     8589934592 Oct  7 13:14 Win2003helper-flat.vmdk
-rw-------    1 root     root        19395 Oct  7 13:14 Win2003helper-Snapshot1.vmsn
-rw-------    1 root     root          406 Oct  7 12:59 Win2003helper.vmdk

The file “Win2003helper.vmdk” contains metadata about the actual harddisk file, which is named “Win2003helper-flat.vmdk”. As you can see we also have a snapshot in place; the .vmsn file contains metadata about the snapshot, and the aforementioned delta disk file is named “Win2003helper-000001-delta.vmdk” (with a matching metafile).

If you’re the curios type, you can do a “cat ” to check out the content of meta files.

5. Make a “thin” clone of the snapshot

Now it’s time to do the magic! Use the “vmkfstool” command to make a clone of the virtual harddrive:

vmkfstools -i Win2003helper.vmdk -d thin Win2003helper_thin.vmdk

The “-d” option tells vmkfstools to make it a thin provisioned disk. The clone will be made from the non-changing snapshot (remember that changes are written to the delta-disk), so we don’t get into trouble with inconsistent drives.

Destination disk format: VMFS thin-provisioned
Cloning disk 'Win2003helper.vmdk'...
Clone: 100% done.

Wait for the cloning to finish. When it’s done, a “ls -l” will reveal the new disk:

-rw-------    1 root     root     8589934592 Oct  7 13:24 Win2003helper_thin-flat.vmdk
-rw-------    1 root     root          437 Oct  7 13:24 Win2003helper_thin.vmdk

You might be surprised to see that the file size is exactly the same at the bloated disk, you were hoping to shrink – but don’t panic, this is only due to the fact that the service console sees the size of the drive, and not how much space it occupies on the storage. Go ahead and browse the storage from the VMware Infrastructure Client, and you should see the true picture

6. Replace the thick disk with the thin clone

Go ahead and overwrite the thick disk with the clone just created:

mv -f Win2003helper_thin-flat.vmdk Win2003helper-flat.vmdk

And then remove the obsolete meta file “Win2003helper_thin.vmdk” either with the Datastore Browser or from the command line:

rm -f Win2003helper_thin.vmdk

7. Delete the snapshot

Finally you can delete the snapshot you created in the Snapshot Manager

Just press “Delete All”, and it will apply all changes that might have happened to the harddrive while we were cloning the disk.

8. Enjoy

If you take a look at the Datastore Browser, you will now find everything cleaned up, and the virtual disk shrunk to fit the actual usage in the virtual machine.

Of cause the file will grow as you add data to your virtual disk, and if you delete a lot of data, you might consider going thru the procedure again, to reclaim that space.

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