perl array size is smaller than it should be

Question

I want to initialize 4^9 (=262144) indices of @clump as 0. So I wrote this:

my $k=9;
my @clump=();
my $n=4**$k;
for(my $i=0;$i<$n;$i++){
   push(@clump,0);
   print "$i ";
}

But it keeps freezing at 261632! I then tried making $n=5^9 (=1953125) and my code stopped at 1952392. So its definitely not a memory issue. This should be simple enough but I can't figure out what's wrong with my code. Help a newbie?

Works fine here: perl -E '$k=9; @clump=(); $n=4**$k; for($i=0;$i<$n;$i++){ push(@clump,0)}' — Håkon Hægland
– Håkon Hægland, Commented Jul 29, 2015 at 21:53
Works for me, as well. Does @clump = (0) x 4 ** $k work for you? — Jim Davis
– Jim Davis, Commented Jul 29, 2015 at 21:58
@ThisSuitIsBlackNot I'm writing a clump finding program using frequency arrays to find the ori site in Ecoli genome. For that I need to find the most frequent 9-nucleotide sequences in a genome file. The easiest way was to convert all possible sequences into corresponding array indices and +1 whenever the program encounters the sequence. — Shubhra Agrawal
– Shubhra Agrawal, Commented Sep 18, 2015 at 17:34

melpomene · Accepted Answer · 2015-07-29 22:25:02Z

9

Suffering from buffering?

When I add a sleep 1000 to the end of your program, stream the output to a file, and read the tail of the file, I also observe the last numbers to be printed are 261632 and 1952392. The remaining output is stuck in the output buffer, waiting for some event (the buffer filling up, the filehandle closing, the program exiting, or an explicit flush call) to flush the output.

The buffering can be changed by one of the following statements early in your program

$|= 1;
STDOUT->autoflush(1);

edited Jul 29, 2015 at 22:25

melpomene

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answered Jul 29, 2015 at 22:16

mob

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1 Comment

Sinan Ünür Over a year ago

Of course, rather than flushing after every a couple of characters, one might want to just use print "\n"; after the loop, or use IO::Handle; ... STDOUT->flush.

Sinan Ünür · Accepted Answer · 2015-07-29 22:40:52Z

3

#!/usr/bin/env perl

use strict;
use warnings;

my $k = 9;
my $n = 4 ** $k;
my @clump = (0) x $n;

print join(' ', @clump), "\n";
printf "%d elements in \@clump\n", scalar @clump;

Or,

#!/usr/bin/env perl

use strict;
use warnings;

my $k = 9;
my $n = 4 ** $k;
my @clump;
$#clump = $n - 1;
$_ = 0 for @clump;

print join(' ', @clump), "\n";
printf "%d elements in \@clump\n", scalar @clump;

Output:

... 
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
262144 elements in @clump

Also, note that initialization with 0 is almost never required in Perl. Why do you need this?

answered Jul 29, 2015 at 22:40

Sinan Ünür

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1 Comment

Shubhra Agrawal Over a year ago

Your first suggestion worked. Thank you for your help :)

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