I refactored the code quite a bit: 
#!/usr/bin/env perl

use strict; 
use warnings; 

my $file = $ARGV[0] || 'pickcpua.dat'; 

open my $CPUFILE, "<", $file or die "Unable to open sorted file $!"; 

my @col_tot;
my @col_num;
my @col_avg;
while (<$CPUFILE>) {
    chomp;
    my @f = split /,/;
    shift @f;   # remove the 1st column
    my $num_cols = scalar @f;
    for my $i (0 .. $num_cols-1) {
        my $val = $f[$i];
        if ($val>0) {
           $col_num[$i]++;
           $col_tot[$i] += $val;
        }
    }
}

for my $i (0 .. $#col_num) {
    $col_avg[$i] = $col_tot[$i]/$col_num[$i];
    print "Column ", ($i + 2), " Average = $col_avg[$i]\n";
}

close $CPUFILE or die; 

my $total = 0; 
$total += $_ for @col_avg; 
print "Average CPU Time for Column for all servers in cpuatest.dat fil
+e is ";
print $total/@col_avg, "\n";

[download]
Update: Oops. After checking math (for a 2nd time!), this is what I get: 
Column 2 Average = 8.27777777777778
Column 3 Average = 8.33222222222222
Column 4 Average = 8.11
Column 5 Average = 8.77
Column 6 Average = 10.4677777777778
Column 7 Average = 17.8433333333333
Column 8 Average = 6.42571428571429
Column 9 Average = 6.66571428571429
Column 10 Average = 6.36571428571429
Column 11 Average = 5.85714285714286
Column 12 Average = 6.01142857142857
Average CPU Time for Column for all servers in cpuatest.dat file is 8.
+46607503607504

[download]
Is this what you are looking for?

In reply to Re: Calculating Column Averages From A CSV File by toolic
in thread Calculating Column Averages From A CSV File by country1

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.