Ack! Sorry to hear this.
The two things that determine memory usage when rendering are:
1) the total number of primitives (spheres, triangles, cylinder [i.e. lines]
etc.)
2) the value of hash_max
#1 may not be easily remedied for your scene
#2 can be improved by setting hash_max to something like 65 or 50.
Rendering will take much longer, but less RAM will be used.
~200k atoms really shouldn't be a problem on a machine with that kind of
RAM, so there is also a chance here you might be experiencing a bug. It
might be worth emailing me a (compressed?) copy of the session file just to
be sure...
I don't see anything wrong with your script.
Cheers,
Warren
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
Jason Vertrees
Sent: Saturday, April 24, 2004 6:50 PM
To: PyMol Users List
Cc: Tzintzuni Garcia I.; Roger B. Sutton
Subject: [PyMOL] Does (PDB) size really matter? (Help!)
PyMolers,
Our setup is a Dual Xeon 3.2 GHz 1GB RAM and Nvidia Quadro
running PyMol 0.95. (Also available, Dual Opteron 240 64-Bit
Linux w/0.95 w/1 GB RAM w/same problems.)
We are trying to render a nifty movie but can't. PyMol keeps
crashing during the render process. The scene had originally
185,000 atoms, but now I've snipped out some cutting it down
to 85,000 or so.
The command ray 800, 600 dies. I then collected all of my
bilayer segment objects into one larger one (so, instead of 8
objects I had one 8x as large, hoping that the reduction in
the number of objects freed up some RAM.)
The movie script for scene1 is
http://www.vertrees.org/~tree/scene1.py.
I'm very new to making movies, but it does what I want.
Here's some PyMol output:
PyMOLcount_atoms
count_atoms: 86220 atoms
PyMOLray
VLAMalloc-ERR: realloc failed
**
**
*** EEK! PyMOL just ran out of memory and crashed. To get
around this,
***
*** you may need to reduce the quality, size, or complexity
of the scene
***
*** that you are viewing or rendering.Sorry for the
inconvenience...
***
**
**
/usr/bin/pymol.com: line 2: 11531 Aborted
/usr/bin/python
/usr/lib64/python2.3/site-packages/pymol/__init__.py $*
Any ideas on how we can keep the movie w/o sacrificing
quality or number of atoms? If need be, I can probably trim
another 3,000-10,000 (max) atoms out.
Much TIA,
-- Jason
--
Jason Vertrees
BSCB Graduate Student @ UTMB, Galveston
javer...@utmb.edu :: http://www.bscb.utmb.edu
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