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It is unfeasible with newer CPUs to just count instructions, as newer CPUs can do multiple per cycle, and have multiple cores and likewise. Cycles per byte is the usual way to measure performance these days. Of course, to make it as fair as possible and comparable to others, the code is only ideally run on one core, turboboost and hyperthreading is turned ...


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If the number of files is fixed, then concatenating the hashes (in a well-defined order) constitutes a hash function. Inverting it requires inverting the hash of one of the files, so if the per-file hash function is a cryptographic hash, then so is that 1000-file hash. If the number of files is variable, then the natural way to combine the hashes would be ...


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What you're looking for is called a Merkle tree. BLAKE2b, a modern hash and an evolution of one of the SHA-3 finalists (BLAKE), supports tree hashing natively. Edit: This may or may not actually be what you're looking for. Initially hashing the tree will take more work ($\mathcal{O}(n\log(n))$ operations) than just hashing the set of hashes, but subsequent ...



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