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  • can there be more than 3 numbers in a line in second file? Commented Oct 6, 2016 at 5:39
  • also, seems like 1st/2nd column numbers are sorted both row wise and column wise, is that always true? Commented Oct 6, 2016 at 5:46
  • If the real data is huge, I'd consider using at least a small perl script instead of awk/cut (because traversing file 2 each time is slow and makes it quadratic), and if it's really huge, I'd write a C program. It's also important to have an idea how large these numbers can get, especially those in file 2. Commented Oct 6, 2016 at 6:58
  • @dirkt I don't think that perl can be faster than awk, see benchmarks in my answer. Commented Oct 6, 2016 at 11:26
  • @rudimeier, agree awk is usually faster than perl, but I feel like someone with better experience would be able to write a perl solution much faster than mine :) Commented Oct 6, 2016 at 11:37