[Chimera-users] [Fwd: creating more memory]

Tom Goddard goddard at cgl.ucsf.edu
Sat Oct 24 01:56:23 PDT 2009

Hi Lori,

  It looks like Chimera is trying to read the full map #0 into memory 
and it is running out of memory.  How big is that map file?  If it is 
several hundred megabytes that is probably the issue.  It is difficult 
to avoid these problems if you work with large data sets.  Chimera 
32-bit versions can only handle about 1 Gbyte of data.  If you have 
large maps of several hundred Mbytes you can easily exceed that.  Or if 
you have models with a few hundred thousand atoms you will run into 
trouble (uses about 2 Kbytes per atom, 100,000 atom = 200 Mbytes).  It 
doesn't matter how much memory your machine has -- the limitation is 
that Chimera uses 32-bit pointers that can only address at most 4 Gbytes 
of memory (and much of that space is used for things other than your 
data, eg libraries, stack, ...).  The only answer is to close some of 
your data our use the 64-bit Linux Chimera.  We plan to distribute a 
64-bit Windows and 64-bit Mac Chimera but that is 6 months or a year away.


> Subject:
> creating more memory
> From:
> Lori Nyland
> Date:
> Fri, 23 Oct 2009 10:24:10 -0400
> To:
> chimera-users
> Hello,
> I have attached an image that shows the command line and the command 
> where I am trying to save an image map of one volume relative to 
> another. I received an error when the operation was executed. The 
> error code is in the image. I noticed that there was an error in 
> memory allocation (toward bottom of error script). So I think I need 
> to allocate more memory. How do I do that?
> Thanks so much!
> Lori

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