I guess the size of your file is imiting. I wrote the code below, and got much better times than the sarcastic guy, but still much too slow for you I think. I based mine on sorting the indexes only, not the entire content of the line. However this does not address your problem of also removing duplicates. I'd be interested in testing what I can up with for your data file. If you want to post it somewhere let me know, and I'll see if I can beat your 4 hour mark.
use strict;
use Tie::File;
use Benchmark::Timer;

our $N ||= 100000;

sub shuffle {
    my $shuffled = ();
    my $numlines = scalar @{$_[0]};
    while ($numlines > 0) {
        my $randomLineNum = int rand $numlines;
        push(@$shuffled, $randomLineNum);
        splice(@{$_[0]}, $randomLineNum, 1);
        $numlines--;
    }
    return $shuffled;
}

open OUT, '>', 'junk.dat' or die $!;
printf OUT "%030d\n", $_ for 0 .. $N;
close OUT;

my @lines;
tie @lines, 'Tie::File', 'junk.dat';
my @indexList = (0..scalar @lines);
my $T = new Benchmark::Timer;

$T->start( "shuffling $N lines" );
my $newOrder = shuffle scalar \@indexList;
$T->stop( "shuffling $N lines" );

$T->start( "Writing New ordered File" );
open NEW, ">sortedJunk.dat";
foreach my $lineNum(@$newOrder){
    print NEW $lines[$lineNum],"\n";
}
$T->stop( "Writing New ordered File" );

$T->report();

[download]

and my results are pretty fast:
numLines,time,writingTime
100,281us total,15.222ms total
1000,1.480ms total,57.048ms total
10000,29.017ms total,559.466ms total
100000,1.922s total,5.969s total
1000000,256.212s total,154.443s total

In reply to Re^7: Strategy for randomizing large files via sysseek by ketema
in thread Strategy for randomizing large files via sysseek by Anonymous Monk

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