[Bioperl-l] Performance of Bio::Species

Jason Stajich jason at bioperl.org
Fri Nov 24 18:16:47 EST 2006


Can we just weaken the references with Scalar::Util? This should  
solve the problem for circular refs.  Is Scalar::Util part of the  
core distro in the min perl we are supporting?

I can add this in Bio::Tree::Node and look around to see where else  
it is a problem.  We just need a simple script to verify it is having  
an effect (i.e. a bug report with this).

-jason
On Nov 21, 2006, at 12:20 PM, Stefan Kirov wrote:

> Hilmar Lapp wrote:
>> On Nov 21, 2006, at 2:37 PM, Sendu Bala wrote:
>>
>>
>>> I don't know if I should hold up release of 1.5.2 for it. Now that
>>> you've
>>> reported on it I'm leaning toward yes, since the new Bio::Species
>>> implementation is one of the major new features of 1.5.2 and it
>>> ought to
>>> work well.
>>>
>>
>> I disagree to some extent. This is a developer release, so not
>> everything is expected to work perfectly.
>>
>> What's not desirable is if fixing this required another entire
>> redesign of the API, so that every dev release introduces  
>> different API.
>>
>> The thing is, you'll really only get trouble reports once you put it
>> out and people start using it in anger. Don't expect to make it
>> perfect before.
>>
>>
>>> Anyway, for the memory leak I have some ideas I haven't tried yet; I
>>> don't know if my efforts will solve the speed issue though.
>>>
>>
>> The memory leak sounds more concerning to me. Under which
>> circumstances would it crash a script or blow throuhg all of say
>> 1-2GB when it should have taken only a tenth of that.
>>
>>
> As I was saying, I did pass ref to an array in the classification  
> (wrong
> parsing):
> push @classification,'sapiens', 'Homo', 'Hominidae', $arrayref;
> and my script took 17-18 GB. I am really surprised it stopped getting
> more RAM and finished successfully. I did not explore further.
> Stefan
>> 	-hilmar
>>
>>
>
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