[Bioperl-l] out of memory issue

Mark A. Jensen maj at fortinbras.us
Wed May 19 13:59:03 UTC 2010

Hi Shalabh and all,
Sorry to comment on an old thread, but Dan Kortschak just pointed me to 
Tie::File. This may be the right solution to this issue. It turns out that 
DB_File will read in the entire file to memory anyway, while Tie::File (by MJD 
of course) works on pieces as it should. See Tie::File in CPAN and also this 
informative post:
cheers all- (someday, maybe next month, I'll return in force)

----- Original Message ----- 
From: "shalabh sharma" <shalabh.sharma7 at gmail.com>
To: "bioperl-l" <Bioperl-l at lists.open-bio.org>
Sent: Wednesday, April 28, 2010 10:13 AM
Subject: [Bioperl-l] out of memory issue

> Hi All,
>       I am trying to make a hash of 38 Million ids but every time i get the
> following message :
> 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

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