RE: [PyMOL] out of memory with PyMOL in batch mode

[Nicolas S. <n....@ib...>]

Warren,
I have tried my script after setting defer_builds_mode and/or -D option
to 2. PyMOL still crashes after approximately the same time than
previously. The error message is slightly different this time :

MoviePNG: wrote /tmp/nsapay_pymol/top0185.png
here 185
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...
***
***************************************************************************

In fact, several pictures have been created, corresponding to the first
185 frames. And pictures have been indeed generated "on the fly", not in
same time.Where is the problem? I ask to PyMOL to generate an important
at each step surface. Can the crash be due to this? (I know, I ask a lot
to PyMOL :-))

Cheers,
Nicolas

Le mer 07/09/2005 =E0 19:46, Warren DeLano a =E9crit :
> Nicolas,
>=20
> PyMOL is probably running out of RAM during geometry construction, which
> is done by default for all 1000 frames (to enable fastest refresh
> rates).  In your case, you want to disable that behavior and only
> generate geometry for the frame being rendered.  This is something I
> added to 0.98:
>=20
> set defer_builds_mode, 2
>=20
> or launch with options: -D 2
>=20
> defer_builds_mode 1 only generates generates geometry when it is needed,
> but then keeps it around.  defer_builds_mode 2 does that and
> additionally actively purges unused geometry.
>=20
> Cheers,
> Warren
>=20
> --
> Warren L. DeLano, Ph.D.                    =20
> Principal Scientist
>=20
> . DeLano Scientific LLC =20
> . 400 Oyster Point Blvd., Suite 213          =20
> . South San Francisco, CA 94080 USA  =20
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> . mailto:wa...@de...     =20
> =20
>=20
> > -----Original Message-----
> > From: pym...@li...=20
> > [mailto:pym...@li...] On Behalf Of=20
> > Nicolas Sapay
> > Sent: Wednesday, September 07, 2005 10:15 AM
> > To: pym...@li...
> > Subject: [PyMOL] out of memory with PyMOL in batch mode
> >=20
> > Dear all,
> > I'm trying to render PNG from -A LOT OF- pdb files (up to 1000!).
> > Fortunately, I can use a Linux cluster with a PBS server. I=20
> > have create a small script that :
> > 	1- loads PDB files (coming from a MD trajectory)
> > 	2- set up the scene (light, color etc.)
> > 	3- renders the movie
> >=20
> > at the end of my script I have thus:
> > mset 1 -1000
> > set ray_trace_frames, 1
> > set cache_frames, 0
> > mclear
> > mpng /tmp/nsapay_pymol/foo
> >=20
> > However, it seems that PyMOL doesn't clear its cache since=20
> > the process fills the memory until crash. No picture is=20
> > rendered and PyMOL clearly tells me that it ran out of=20
> > memory. It seems to me that with the cache turned off, frames=20
> > should be rendered successively and not stored in the memory.=20
> > I have make some tests, it seems that PyMOL indeed loads all=20
> > PDB but crashes just after the mpng command line. So, is the=20
> > problem could be due to an error in my script? Or may be=20
> > because my system is quite large (> 15000 atoms * > 1000 frames!).
> > Any suggestion will be welcome!
> >=20
> > Nicolas
> >=20
> > PS : congratulation to PyMOL authors! It's a well-conceived=20
> > and well documented software.
> > =20
> > --
> > _ Nicolas Sapay ____________________________________________
> >   Ph.D sudent in structural bioinformatics
> >   Institut de Biologie et Chimie des Proteines
> >   CNRS - Claude Bernard University, Lyon I
> >=20
> >   > contact :
> >     7, Passage du Vercors      Tel: +33 (0)4 72 72 26 46
> >     69367-F Lyon cedex 07      Fax: +33 (0)4 72 72 26 04
> >     France                     Web: http://pbil.ibcp.fr/
> >=20
> >=20
> >=20
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> >=20
> >=20
> >=20
--=20
_ Nicolas Sapay ____________________________________________
  Ph.D sudent in structural bioinformatics
  Institut de Biologie et Chimie des Proteines
  CNRS - Claude Bernard University, Lyon I

  > contact :
    7, Passage du Vercors      Tel: +33 (0)4 72 72 26 46
    69367-F Lyon cedex 07      Fax: +33 (0)4 72 72 26 04
    France                     Web: http://pbil.ibcp.fr/