Of course your problem can be fixed with code. It's not that you are asking for something that's not solvable on a Turing machine. As for wether you need to implement a different algorithm, that's up to you. I described an efficient algorithm. If you find an implementation of a naive algorithm (matching everything from one file with every thing from the other) fast enough, then stick with it. But I got the impression you had some very large datasets. And very large times very large is big.

As for the algorithm being sophisticated, that depends on what you find sophisticated. I don't find the algorithms itself sophisticated, but then, I did research in this field for a few years. And I wouldn't do the implementation in an evening either. But I'm a slow coder.

Abigail

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