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I am using tree hash mode of Skein on a 16 core processor. Will it automatically employ parallelism using more than one cores or do I have to use multi-threading within the tree hash for parallel processing?

Also, the tree hash mode requires three parameters: leaf size encoding, fan-out encoding and tree height. Except for the last one, I am confused about the other two parameters, what are they exactly?

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That depends on your implementation ... the specification doesn't dictate using multi-threading. –  Paŭlo Ebermann Sep 27 '12 at 18:00
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On multi-threading: Read the code. As Paulo writes, that's up to the implementation. Read the source code of your library and see for yourself what it is doing; it shouldn't be too hard to figure it out.

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