08-13-2014
What's the exact contents of each file?
Right now, you're literally running millions of greps, comparing each ID to every other ID. That's a huge waste of time, obviously. You only really need to compare each ID to itself.
Because it seems to me that you're just looking for IDs that are in both files. If each ID only occurs once in each file, pull the IDs out of each file, combine them into one file, sort them, and only count IDs that are duplicated in the combined file.
Or you can figure out how to use the "join" utility, though that may not be any faster than what you're already doing, although it does have the huge advantage of not having to fork() and exec() a new process millions of times.
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