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During the installation of Lubuntu I chose to encrypt my whole HDD (not just the /home folder). Now it feels like my system has slowed down a lot. Especially the startup time of programs increased.

Does this encryption also slow down programs (after loading) which neither read from nor write to the HDD?

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It depends on a few things. Encrypting a disk CAN make it slower. For example, if you have an SSD capable of 500mb/sec and then do full disk encryption on it using some crazy long algorithm you might get FAR below that max of 500mb/sec. I've attached a quick benchmark from TrueCrypt.

There is CPU/Memory overhead for any encryption scheme.

enter image description here

You can see if I just used AES things are going to be pretty fast... but Serpent-Twofish-AES is many factors slower.

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My harddrive is slower than my CPU using most of encryption algorithms. But my question was aimed at harddrive independent programs. Is the RAM encrypted too? – Stein Apr 20 '13 at 20:22
@Stein No, the RAM isn't encrypted. Encrypting the disk ties up the CPU for disk I/O (not much on recent CPUs), but doesn't otherwise slow the execution of programs when they are fully running off RAM. – Gilles Apr 20 '13 at 23:49

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