Nicolas, 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:
set defer_builds_mode, 2 or launch with options: -D 2 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. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Nicolas Sapay > Sent: Wednesday, September 07, 2005 10:15 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] out of memory with PyMOL in batch mode > > 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 > 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 > > 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 > > However, it seems that PyMOL doesn't clear its cache since > the process fills the memory until crash. No picture is > rendered and PyMOL clearly tells me that it ran out of > memory. It seems to me that with the cache turned off, frames > should be rendered successively and not stored in the memory. > I have make some tests, it seems that PyMOL indeed loads all > PDB but crashes just after the mpng command line. So, is the > problem could be due to an error in my script? Or may be > because my system is quite large (> 15000 atoms * > 1000 frames!). > Any suggestion will be welcome! > > Nicolas > > PS : congratulation to PyMOL authors! It's a well-conceived > and well documented software. > > -- > _ 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/ > > > > ------------------------------------------------------- > SF.Net email is Sponsored by the Better Software Conference & > EXPO September 19-22, 2005 * San Francisco, CA * Development > Lifecycle Practices Agile & Plan-Driven Development * > Managing Projects & Teams * Testing & QA Security * Process > Improvement & Measurement * http://www.sqe.com/bsce5sf > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > >
