If you're on Unix, there's no need for Perl. (Windows has both the Unix utilities and Cygwin.) 
sort file1.csv > file1.sort.csv
sort file2.csv > file2.sort.csv
comm file1.sort.csv file2.sort.csv

[download]

Plus, 61k lines isn't very large at all ... I'm curious as to how you were comparing them originally that you felt was too slow. Maybe your initial algorithm was borked. Could it have been something like 

open FIRST, "first.csv";
while (my $line = <FIRST>) {
    open SECOND, "second.csv";
    while (my $otherline = <SECOND>) {
        if ( $line eq $otherline ) {
            print "Found a match!\n":
        }
    }
    close SECOND;
}
close FIRST;

[download]
Because that's really slow!

My wife's blog

In reply to Re: Binary Search by dragonchild
in thread Binary Search by dave_pl

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.