If you know there's going to be a large number of swaps, why not make a set of array subscripts and swap those around, then output in whatever the final order is?
use strict;
use warnings;
my (@nums, @index, $x, $y);
# CREATE MATRIX
push @nums, [1..12] for 1..12;
# CREATE INDEX
@index = (0..11);
# PERFORM RANDOM SWAPS
for (1..20) {
$x = int rand 12;
$y = int rand 12;
swap(\@index, $x, $y);
}
# OUTPUT IN FINAL ORDER
for $x (0..$#nums) {
print $nums[$y][$_].' ' for (@index);
print "\n";
}
sub swap {
my ($p, $x, $y) = @_;
my $t = $p->[$y];
$p->[$y] = $p->[$x];
$p->[$x] = $t;
}