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I have 500 GB Sized Confidential directory stored in an external HDD. Which is fastest method to encrypt/decrypt it? I have checked openssl,but it takes too much time.Please advice

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You should probably consider using encrypted file-systems, rather than crypting files individually. Consider something like en.m.wikipedia.org/wiki/Encfs or similar. – tink May 25 '13 at 18:51
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When openssl is used to encrypt something, it's a pretty direct plaintext-in-ciphertext-out scenario without much other overhead. It doesn't really get any faster than that! By the way, you should consider something with a little more of a user interface than openssl, like GnuPG.

What will make the biggest difference no matter what you use is disk I/O. If at all possible, write the result to another disk. (If you want, you can copy it back to the first disk once it is done.) This will be much, much faster than reading from one disk and writing back to the same disk.

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