Well, ^ doesn't mean the same as \n? at all. Like not even close. According to Programming Perl 3rd edition pages 150 and 159, ^, when used with the /m modifier, means to match after embedded newlines or the beginning of the string.
\n? means something akin to possibly match a newline, but maybe not. That doesn't provide the engine with any understanding of where to match. Had you said something like /\n(.*$pat.*\n)/, you would have been better off (except for not matching the first line). Of course, with /m, you should be able to do /^(.*$pat.*)$/omsg and it should be about as efficient as my regex.
With regexes, it's always better to be as explicit as possible. This will allow the engine to make a number of optimizations. Some of those optimizations, as you have found out, can mean the difference between 2500 seconds and 23 seconds.
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Good question. I guess using ^ to match newlines is probably just not very well optimized in the engine.
The usual trick to make regexes faster is to be as explicit as you can be (like spelling out the newlines) and it helped here. I don't know enough about perl's regex internals to really explain why it works as well as it does in this case.
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