RE: [PyMOL] pymol crashes with large pdb files

That's likely the problem.

If you need to reduce RAM consumption during raytracing (at the cost of
performance), try reducing hash_max to 80 or 60.

set hash_max,60

Cheers,
Warren


--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

> -----Original Message-----
> From: pym...@li... [mailto:pymol-users-
> ad...@li...] On Behalf Of an...@bi...
> Sent: Wednesday, June 25, 2003 12:28 PM
> To: Nat Echols
> Cc: pymol
> Subject: Re: [PyMOL] pymol crashes with large pdb files
> 
> Limited physical memory might indeed be the problem.
> When I ray-trace under WinXP, memory usage increases sharply (to about
> 500MB) and after a second or so, pymol crashes.
> When I ray-trace under linux, almost all physical memory (1GB) is
being
> used. Barely 40MB available.
> 
> We should be getting new computers next week. We'll see if 2GB will do
the
> trick for Windows.
> 
> 
> Andreas
> 
> 
> >> Now there is a twist to the story. We also run linux (redhat with
> 2.4.18
> >> kernel) on a 2 CPU 930MHz (1GB RAM, Nvidia GeForce2 GTS) PIII.
Working
> >> speed is much slower but no crashes when ray-tracing from the exact
> same
> >> pml script.
> >> Can it be that linux makes better use of its physical memory or
that
> the
> >> 2GB of swap make the difference?
> >
> > When you ray-trace an image, PyMOL will tell you exactly how much
memory
> > it's using.  My suspicion is that this is painfully close to the
> physical
> > memory limit.  From what I understand, swap space does not give you
more
> > memory but Linux will transfer idle programs to swap, freeing up
more
> > RAM for PyMOL.  I have no idea how Windows works (other than
"badly").
> >
> > 'top' in Linux or the Task Manager in WinXP should tell you how much
> > physical memory is being used at any time.
> >
> >
------------------------------------------------------------------------
> ----
> > Nathaniel Echols
> > Programmer
> > na...@bi...
Gerstein
> > Lab
> > 203-589-6765                                                 Yale
> > University
> >
------------------------------------------------------------------------
> ----
> 
> 
> 
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