If I use whole disk encryption, will I notice a drop in performance?
And what about for a SSD?
And I see that there is a option in my bios that enables Intel AES-NI does this have any effect on my encryption?
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You will notice a slowdown as you can see in these benchmarks that we done by Phoronix a few months ago (these benchmarks were done on an SSD by the way): http://www.phoronix.com/scan.php?page=article&item=linux311_disk_encryption&num=1
As you can see, performance can drop rather drastically. Unfortunately, I have no experience with Intel AES-NI, so I can't say what kind of effect that option would have. But I do think that if you're working with encrypted files you will always see some kind of slowdown since it needs to decrypt your stuff all the time (or at least at boot time)