If you could provide something we can actually run to see the performance issues ourselves, we could provide specific suggestions - see Short, Self-Contained, Correct Example. Until then, some general optimization tips:

• Use Devel::NYTProf to locate the places where your code is spending the most time.
• Consider using a different XML parser, since XML::LibXML will load the entire DOM structure into memory by default, while XML::Twig is geared more towards processing a large file piece by piece, without loading the whole file into memory.
• I see you doing foreach over an array of apparently 1 million (?) lines - this means you're keeping those lines in memory. It would most likely be more efficient to use a while(<$filehandle>) loop to read the file line-by-line, without loading it all into memory.
• I see you repeating some findnodes calls twice, causing that effort to be doubled. Consider storing the results in a local variable so you can use it more than once.

If you have a input file of 1 million lines, consider that maybe it'll just take some time to process, and that 100% CPU consumption during that time is normal.

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