You could verify what part of your code is being slow either by using the Time::HiRes module to time different parts of your code: 
use Time::HiRes qw(time);

use vars qw($then);
sub timepart
{
  my($partname)=@_;
  my $now = time;
  if ($partname)
  {
    $time{$partname} += $now - $then;
  }
  $then = $now;
}

timepart();
foreach my $line (@FILE) {
   timepart('loop');
    if (($dot % 1000) == 0) {
      print STDERR ".";
   }
   timepart('mod');

   $line=~/^(\S*) [0-9.]* (.*)$/o;
   my ($class, $feature_vector) = ($1, $2);
   timepart('regex');
   my %case;
    
   $case{'class'}=$class;
   timepart('createcase');
   foreach my $feature (split /\s+/, $feature_vector) {
      $case{'fv'}{$feature}=1;
   }
   timepart('feature');
   
   push @cases, \%case;
   timepart('pushcase');

   $dot++;
}
print "\n";
while(my($k,$v)=each(%time))
{
  printf "%10s: %10.6f\n",$k,$v;
}

[download]
or by reducing your code to a very small amount and seeing if it's still slow: 
for $i in (1..2_000_000)
{
  my %case;
  push(@r,\%case);
}

[download]

In reply to Re: Slowness when inserting into pre-extended array by sgifford
in thread Slowness when inserting into pre-extended array by ryangabbard

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