This should work

#!/usr/bin/perl

use strict;
use warnings;

open IN, 'data.txt' or die$!;
my @colSum;

while(<IN>){
    chomp($_);
    my @colArray = split(/\s/,$_);
    for(my $i = 0; $i <= $#colArray; $i++){
        $colSum[$i] += int($colArray[$i]); 
    }
}

foreach my $ j(0 .. $#colSum){
    print "Sum for column",$j,"is: ",$colSum[$j],"\n";
}
[download]

What you were trying to do was not correct. You were taking the entire line and was adding to another line. $_ takes it as a string and if you convert into a int type also then it will not convert according to your logic because there will be spaces between them. Therefore, you need to take it into an array and compute the sum of column by adding to the previous element using loop.