[Bioperl-l] Performance of Bio::Species

Stefan Kirov stefan.kirov at bms.com
Tue Nov 21 15:20:40 EST 2006


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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