[Bioperl-l] out of memory issue

Dave Messina David.Messina at sbc.su.se
Wed Apr 28 11:23:56 EDT 2010

Hi Shalabh,

The problem is quite clear, that you're running out of memory, so you need to find out why.

A lot depends on how big your IDs are and the associated values you're storing. And Perl also has some overhead of its own that might taking a lot more space than expected.

Try installing the Devel::Size module and using its total_size function.

Look at how many bytes a hash of, say 10,000 or 100,000 of your records instead of all 38 million.

something like

use Devel::Size qw(total_size);

my %hash;
print "Empty: ", total_size (\%hash), " bytes\n";

# fill %hash here

print "Full: ", total_size (\%hash), " bytes\n";


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