I'm not quite sure how you're comparing things, but won't something like the following do: 
$ perl -ple 's/\s+/ /g' today | sort > today.s
$ perl -ple 's/\s+/ /g' yesterday | sort > yesterday.s
$ comm -3 today.s yesterday.s

[download]
Or as a one liner (bash syntax): 
$ comm -3 <(perl -ple 's/\s+/ /g' today | sort) <(perl -ple 's/\s+/ /g
+' yesterday | sort)

[download]

In reply to Re: Compare large files by JavaFan
in thread Compare large files by boardryder

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