You need to calculate the average outside the foreach loop.

use warnings;
use strict;

# sub get_avr {
# 'get' implies that the sub is returning a value?
sub print_avr {
    my ( $cluster ) = @_

#   open(IN, "$outputfile");
# Where does $outputfile come from?  You should pass this value
# to the subroutine instead of using globals.  What happens when
# you try to read from an invalid filehandle?
    open IN, '<', $outputfile or die "Cannot open '$outputfile' $!";

    my %data;
    while ( <IN> ) {
        my ( $hour, $cpu ) = /(\d+):\d+\s+([\d.]+)/ or next;
        $data{ hour }{ total } += $cpu;
        $data{ hour }{ count }++;
        }

    close IN;

    for my $hour ( sort { $a <=> $b } keys %data ) {
        print "$cluster $hour:00 ", $data{ $hour }{ total } / $data{ $
+hour }{ count }, "\n";
        }
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