You can break up the input file into records by setting the record seperator,

#!/usr/local/bin/perl 

my ($in_filename, @records) = 'graph_set.out';
{
    local $/ = ' PLUTO4 finished';
    my $start = ' Final graph set matrix';
    open IN, '<' $in_filename or die "Can't open $in_filename: ", $!;
    @records = map {
        substr $_, index( $_, $start) + length( $start}
    } <IN>;
    chomp @records;
    close (IN);
}
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Without seeing your data, I can't say much about your regex or how it parses.

After Compline,
Zaxo