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MathGroup Archive 2004

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Re: Excessive Mathematica memory use, revisited.

  • To: mathgroup at smc.vnet.net
  • Subject: [mg46873] Re: Excessive Mathematica memory use, revisited.
  • From: Jens-Peer Kuska <kuska at informatik.uni-leipzig.de>
  • Date: Fri, 12 Mar 2004 23:39:18 -0500 (EST)
  • Organization: Universitaet Leipzig
  • References: <c2rnjr$p13$1@smc.vnet.net>
  • Reply-to: kuska at informatik.uni-leipzig.de
  • Sender: owner-wri-mathgroup at wolfram.com

Hi,

if you have a 16 bit image that need 500 MByte, Mathematica will
store the 16 bit number as 32 bit integers and the Mathematica kernel
needs 1 GByte. In allmost all cases Mathematica will try to
make a copy of the data when a function is called and a single copy
will overflow your physical memory.

The only solution is to write a C/C++ MathLink program that store
the data as 16 bit shorts and add some C functions to manipulate
the data. 

I have used this technique several times for huge volume data and
Mathematica serve only as a comfortable command interface.

Or can you split the image in smaller sections ??

Regards
  Jens


"Virgilio, Vincent" wrote:
> 
> Hello,
> 
> First, thanks to Jens-Peer Kuska for responding to this issue back in
> September,
> 
> http://forums.wolfram.com/mathgroup/archive/2003/Sep/msg00125.html.
> 
> I am now working with a much more powerful machine: P4 2.6 GHz, 2GB RAM,
> Windows XP, Mathematica 5.0.0.
> 
> My goal is still to manipulate very large images. Currently I am trying
> to use Experimental`BinaryImport to import an ~ 500MB image into
> Mathematica. Each sample is an unsigned 16-bit integer.
> 
> I start the Windows Task Manager, display the process list, and sort by
> memory usage.
> 
> Then, after issuing the following commands to a cold kernel, I watch the
> Mathematica kernel rise to the top of the above list, consume chunks of
> memory in steps of maybe 20MB, and exhaust physical memory.
> 
> <<ImageProcessing`
> 
> $MessagePrePrint=Short;
> 
> $HistoryLength=0;
> 
> <<Utilities`MemoryConserve`
> 
> Off[MemoryConserve::start];Off[MemoryConserve::end]
> 
> <<Experimental`
> 
> image=ToPackedArray[BinaryImport["500MBimage",{"UnsignedInteger16"...}]]
> ;
> 
> There is memory exhaustion with or without ToPackedArray[].
> 
> I could understand this behaviour if Mathematica is storing each sample
> in a node of some sort of tree. Then the data volume would be multiplied
> by some factor determined by the tree node size. If this is the case, is
> there a way to avoid this, during import, with packed arrays?
> 
> Is there anything obviously wrong or inefficient in the above code? I've
> tried to incorporte Jens' suggestions. One of his was to use Hold[]
> wherever possible; I can't see where it would be productive to do that
> here.
> 
> Note, I see similar behaviour on a smaller scale with much smaller
> images (14MB, per earlier mail). Which is not a problem since the memory
> ceiling has gone up considerably.
> 
> Perhaps 2GB is simply inadequate for this task, since I don't expect
> Mathematica to use a data tile cache. Other products do, but then they
> target a much more specific application domain.
> 
> Regards and thanks,
> 
> Vince Virgilio
> 
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