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 à 19:46, Warren DeLano a écrit : > 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 > > > > > > -- _ 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/
