[buster-discuss] ME and memory

[Clemens Vonrhein]

Hi,

sorry for the late response!

You probably have also high(ish) resolution data? What does the
sampling rate (in the LIST.html) tell you? The ME calculation can get
REALLY big.

So you might want to run a ME job at lower resolution (to cut down on
the sampling rate). If you're after missing loops/domains, even
2.5-3.0A data should tell you something.

Cheers

Clemens

On Mon, Nov 21, 2005 at 10:22:53AM -0500, jjwarren at duke.edu wrote:
> Hi-
> 
> I have been trying to use buster to refine an incomplete structure and it
> seems to be working well, but crashes if I try to do maximum entropy
> refinement.  I get the following error:
> 
> 
>    Allocated BUFFER of size:  1732.500 Mb.
>  Not enough memory to allocate BUFAUX of size:  1732.500 Mb.
>   Program stopped.
>  closesok message: time spent in tree = 2097.88 (user)  15.54 (sys)
>             Error - Not enough memory to allocate BUFAUX of size: 1732.500
> Mb.
> 
> 
> I get the same error on two different linux machines which have different
> amounts of memory.  The larger of the two has 2 Gb RAM, so I am assuming
> that the problem is with memory allocation in the software and not with
> the computers' physical memory.  Anyone have a fix/work around, or do I
> need to try to get a custom version of the program(s)?
> 
> Pertinent Stats:
> Running Buster 1.0.2 for linux on Fedora Redhat or SuSe Linux 9.0
> Protein + missing atoms ~ 240 kDa
> Unit Cell: 260 260 260 90 90 90, with one molecule in the AU.
> 
> Also, ME works fine with the tutorial data.
> 
> Thanks in advance for your help,
> 
> Josh
> 
> 
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> 

-- 

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* Clemens Vonrhein, Ph.D.     vonrhein AT GlobalPhasing DOT com
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