in reply to Why does Perl get slower when building a larger hash? (Not due to the memory swapping)
G'day chialingh,
Welcome to the monastery.
The first thing I'd suggest doing is adding use warnings; (warnings) after use strict; and fix up problems that are reported. There may be others, but a couple that grabbed my attention were close IN; (a filehandle that is never opened) and my %hash1; ... my %hash1 ... (declared twice in same scope - ditto for %hash2).
One place where I believe you're doing unnecessary processing is:
my %file_genes = %$file_gene_ref; ... %hash1 = %{$file_genes{$m1}}; %hash2 = %{$file_genes{$m2}}; ... $intersection{$_} = $hash1{$_} if exists $hash2{$_}; ...
Rather than performing all those hash dereferences, I believe you could simply write something like:
$intersection{$_} = $file_gene_ref->{$m1}{$_} if exists $file_gene_ref->{$m2}{$_};
You'd need to handle other references to %hash1 and %hash2 in a similar fashion. At the very least, I don't believe you need to create the intermediate hash %file_genes: you could just create %hash1 and %hash2 directly, like this:
%hash1 = %{$file_gene_ref->{$m1}}; %hash2 = %{$file_gene_ref->{$m2}};
If that doesn't help, you'll need to profile your code. Devel::NYTProf may be a good place to start; other modules listed under CPAN - Development Support might be useful.
-- Ken
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Re^2: Why does Perl get slower when building a larger hash? (Not due to the memory swapping)
by chialingh (Initiate) on Mar 03, 2013 at 20:44 UTC |