[buster-discuss] ME and memory

[Clemens Vonrhein]

Hmmm ... on the 2Gb machine, try cutting at 3.2 and if that doesn't
work maybe at 3.4A?

Cheers

Clemens

On Mon, Nov 28, 2005 at 03:09:15PM -0500, jjwarren at duke.edu wrote:
> The Shannon Samplig Rate is 384 384 384.  Is that what you're asking for?
> 
> Unfortunately, the data is already cut at 3 A.  It only goes to 2.8 or so,
> anyway.  Any other thoughts?  Thanks!
> 
> Josh
> 
> 
> On Mon, 28 Nov 2005, Clemens Vonrhein wrote:
> 
> > 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
> > >
> > >
> > > _______________________________________________
> > > buster-discuss mailing list
> > > buster-discuss at globalphasing.com
> > > http://www.globalphasing.com/mailman/listinfo/buster-discuss
> > >
> >
> > --
> >
> > ***************************************************************
> > * Clemens Vonrhein, Ph.D.     vonrhein AT GlobalPhasing DOT com
> > *
> > *  Global Phasing Ltd.
> > *  Sheraton House, Castle Park
> > *  Cambridge CB3 0AX, UK
> > *--------------------------------------------------------------
> > * BUSTER Development Group      (http://www.globalphasing.com)
> > ***************************************************************
> >
> 
> _____________________________________________
> -  Joshua Warren, PhD (jjwarren at duke.edu)   -
> -        212 Nanaline H. Duke               -
> -                 DUMC                      -
> -        home: (919) 918 7860               -
> -        work: (919) 681 5266               -
> _____________________________________________
> 

-- 

***************************************************************
* Clemens Vonrhein, Ph.D.     vonrhein AT GlobalPhasing DOT com
*
*  Global Phasing Ltd.
*  Sheraton House, Castle Park 
*  Cambridge CB3 0AX, UK
*--------------------------------------------------------------
* BUSTER Development Group      (http://www.globalphasing.com)
***************************************************************