Glad you found a solution to your problem!

As far as the memory leak, how big is @array? Does a loop like this leak memory?

foreach my $i (0..$#array)
{
  open(FH,"> temp$i") or die "open: $!";
  print FH $array[$i];
  close FH;
}
[download]

A few other random comments:

• Do you realize that if($ctr2=100000) will always be true, since = is the assignment operator not a comparison operator?
• A hash is a strange data structure to store an ordered list of things, like lines in a file. An array is more appropriate.
• Even better, rather than keeping 100000 lines in memory at a time, just keep the output file open, then print lines to it as you read them.
• Also consider using use strict and the -w flag, and using lexical variables for your loops:

  for my $line (@array){
  

  If you are doing something you don't realize, like causing a memory leak, this will often tell you. It's also clearer that a memory leak isn't happening when it will disappear immediately after the loop.
• Or see if you can get sort(1) to do this for you.