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The easiest way to avoid problems when you remove snapshots is to prevent them from happening in the first place. Removing snapshots that are no longer needed is one way to avoid these issues, but let's face the facts: Sometimes problems occur.
There are a few things to watch out for that could cause you to run into trouble when it comes to snapshot removal. It's important to keep the snapshot chain small. Use one snapshot and then remove it when it's no longer needed. If you have a large chain of 20 or 30 delta-files -- and, in the worst case scenario, the files are very large -- that's a recipe for snapshot removal disaster.
The other things data center admins should be wary of is space. Make sure there is enough disk space available on the data store where you store VM disk files. It requires additional space to remove snapshots, and you'll need even more disk space to track changes made during the removal process when the VM is powered on. If you don't have enough space, there will be errors during snapshot removal.
If you are removing a large number of snapshots and/or there is a large amount of data involved, I suggest you perform the snapshot removal with the VM powered off, if possible. Powering the VM off eliminates the need for the vmkernel to store data that is changed during the snapshot removal process, since no data is changed in the powered off VM.
Whether the VM is powered off or not, it's key that the snapshot removal process take place during off-peak hours. That way, the process won't stress the I/O channel and the CPU resources of the ESXi host.
To avoid issues when you remove snapshots, make sure there is enough disk space available on the data store in which the VM's files are located before you begin the process. You may need to migrate another VM away from the data store to clear up some space.
If the VM has a lot of delta files and a lot of data to commit to memory, the best option is to clone everything to a new VM. If you do this, the VM should be powered off because you don't want clients connecting to the OS to modify any VM data. The VM clone takes the current state of the original VM and reads all of the data without taking any snapshots into account.
When the cloning process is complete, you can delete the original VM; there's no cleanup needed for those snapshots. One caveat is that you lose the network card configuration in the new VM clone. Because of this, you might have to reestablish networking in the OS.
If you continue to have problems when you remove snapshots, you may want to start from the beginning and figure out how snapshots work. Your issue could have to do with the anatomy of VM snapshots or it might revolve around the creation of snapshots instead of removal.
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