• How many even columns do you have?
• How many odd columns do you have?
• Are you just comparing items on the same line? If so, there may be no need to read all lines of your large input file into memory at once.
• Or, do you need to compare an item on one line to items on all other lines?
• Are you comparing strings or numbers?
• What are you using the 1st column for?
• Show a small sample of your input (fewer than 10 lines, fewer than 10 columns). Creating a small sample for yourself will make it easier for you to debug your own code, so the extra effort should pay off.

Update: here is some example code to read the whole file into a data structure (HoHoA):

use warnings;
use strict;
use Data::Dumper;

my %data;
while (<DATA>) {
    my ($id, @cols) = split;
    for my $i (0 .. $#cols) {
        my $type = ($i % 2) ? 'odd' : 'even';
        push @{ $data{$id}{$type} } , $cols[$i];
    }
}
print Dumper(\%data);

__DATA__
a 1 2 3 4 5 6
b 9 8 7 6 5 4
[download]

$VAR1 = {
          'a' => {
                   'even' => [
                               '1',
                               '3',
                               '5'
                             ],
                   'odd' => [
                              '2',
                              '4',
                              '6'
                            ]
                 },
          'b' => {
                   'even' => [
                               '9',
                               '7',
                               '5'
                             ],
                   'odd' => [
                              '8',
                              '6',
                              '4'
                            ]
                 }
        };
[download]