I wrote a code to re arrange a two column file into a 4 column file. It turns out that when I use a large input the program crashes and spits the following message:

. 
*** malloc: vm_allocate(size=262144) failed with 3<br>
*** malloc[591]: error: Can't allocate region<br>
Out of memory!

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The whole purpose is to randomize elements within each list of a huge list of lists and then pair within a list two by two elements.

My guess is that the problem is in the last loop of the following code. Could somebody please help me solving this problem? I ruan perl in MACOX 10.2.8 and , G4, 768 MB ram.

Thanks

@total = (); #this is an array of arrays 
@haplotypes=();
$currentPop = 0;
$sampleSize={};  # This will hold the sample size for each population 
+               

while(<IN>) {        
  chomp;

  if (/^(\-{0,1}\d+\t-{0,1}\d+)/) {
                                                  
     $sampleSize{$currentPop}++;
     @temp = split;
     push @{$haplotypes{$currentPop}}, [@temp];<p>
 
  } elsif (/segsites: (\d+)/) {
     $currentPop++;
     push @total, $currentPop;
  }    
}

foreach $_ (@total) { 
  for($i = 0; $i < $sampleSize{$currentPop}; $i++){
    $Rand=rand(int(@{$haplotypes{$_}}));
    $temp=splice (@{$haplotypes{$_}}, $Rand, 1);
    push @{$RandHapl{$_}}, $temp;
  }
}

[download]

20040804 Janitored by Corion: Put code tags around code, reduced indentation

20040804 Janitored by davido: Put code tags around error message (necessary due to square brackets).

In reply to memory leak by Juba

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