[Bioperl-l] out of memory issue

Mark A. Jensen maj at fortinbras.us
Wed Apr 28 12:24:51 EDT 2010


You might look then in particular at a DB_File tie, with BTREE, check out the 
docs on Cpan
----- Original Message ----- 
From: "shalabh sharma" <shalabh.sharma7 at gmail.com>
To: "shalabh sharma" <shalabh.sharma7 at gmail.com>; "bioperl-l" 
<Bioperl-l at lists.open-bio.org>
Sent: Wednesday, April 28, 2010 11:55 AM
Subject: Re: [Bioperl-l] out of memory issue


Hi,
@ Andreas: Actually that is kind of search thing, i am making that hash so i
can search values out of it.
I will try to look what Dave and Mark has suggested , if it doesn't work
then i will use some other alternative like batches.

Thanks
Shalabh


On Wed, Apr 28, 2010 at 11:49 AM, Andreas Kahari <ak at ebi.ac.uk> wrote:

> On Wed, Apr 28, 2010 at 10:13:11AM -0400, shalabh sharma wrote:
> > Hi All,
> >        I am trying to make a hash of 38 Million ids but every time i get
> the
> > following message :
>
> Why would you want to do that?  What is the application and would you
> be able to solve it by either re-ordering the things you doing or doing
> things in batches?
>
>
> Andreas
>
> >
> > perl(191) malloc: *** mmap(size=16777216) failed (error code=12)
> > *** error: can't allocate region
> > *** set a breakpoint in malloc_error_break to debug
> > Out of memory!
> >
> > I am working on MacOX 10.5.8 with 4GB of memory.
> >
> > I would really appreciate if anyone can help me out.
> >
> > Thanks
> > Shalabh
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
>
> --
> Andreas Kähäri, Ensembl Software Developer
> European Bioinformatics Institute (EMBL-EBI)
> Wellcome Trust Genome Campus, Hinxton
> Cambridge CB10 1SD, United Kingdom
>

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