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RE: [PyMOL] out of memory with PyMOL in batch mode
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From: Warren D. <wa...@de...> - 2005-09-08 16:18:56
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Nicholas, Hmm. At this point, I'm stumped. PyMOL may indeed be leaking = memory...we'll have to take a look at this. Could you please email me = your complete script/program so that we can attempt to reproduce the = problem. In the meantime, I suggest breaking up the rendering job into smaller = chunks or using a Python loop to load and render each frame separately, = being sure to disable auto_zoom so that the camera doesn't move around = between frames. Cheers, Warren -- Warren L. DeLano, Ph.D. =20 Principal Scientist . DeLano Scientific LLC =20 . 400 Oyster Point Blvd., Suite 213 =20 . South San Francisco, CA 94080 USA =20 . Biz:(650)-872-0942 Tech:(650)-872-0834 =20 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:wa...@de... =20 =20 > -----Original Message----- > From: Nicolas Sapay [mailto:n....@ib...]=20 > Sent: Thursday, September 08, 2005 5:32 AM > To: Warren DeLano > Cc: pym...@li... > Subject: RE: [PyMOL] out of memory with PyMOL in batch mode >=20 > Warren, > I have tried my script after setting defer_builds_mode and/or=20 > -D option to 2. PyMOL still crashes after approximately the=20 > same time than previously. The error message is slightly=20 > different this time : >=20 > MoviePNG: wrote /tmp/nsapay_pymol/top0185.png here 185 > VLAMalloc-ERR: realloc failed > ************************************************************** > ************** > *** EEK! PyMOL just ran out of memory and crashed. To get=20 > around this, > *** > *** you may need to reduce the quality, size, or complexity=20 > of the scene > *** > *** that you are viewing or rendering. Sorry for the=20 > inconvenience... > *** > ************************************************************** > ************* >=20 > In fact, several pictures have been created, corresponding to=20 > the first > 185 frames. And pictures have been indeed generated "on the=20 > fly", not in same time.Where is the problem? I ask to PyMOL=20 > to generate an important at each step surface. Can the crash=20 > be due to this? (I know, I ask a lot to PyMOL :-)) >=20 > Cheers, > Nicolas >=20 > Le mer 07/09/2005 =E0 19:46, Warren DeLano a =E9crit : > > Nicolas, > >=20 > > PyMOL is probably running out of RAM during geometry construction,=20 > > which is done by default for all 1000 frames (to enable fastest=20 > > refresh rates). In your case, you want to disable that=20 > behavior and=20 > > only generate geometry for the frame being rendered. This is=20 > > 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=20 > > needed, but then keeps it around. defer_builds_mode 2 does=20 > that and=20 > > 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 > > . Biz:(650)-872-0942 Tech:(650)-872-0834 =20 > > . Fax:(650)-872-0273 Cell:(650)-346-1154 > > . mailto:wa...@de... =20 > > =20 > >=20 > > > -----Original Message----- > > > From: pym...@li... > > > [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 have=20 > > > 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 the=20 > > > process fills the memory until crash. No picture is rendered and=20 > > > PyMOL clearly tells me that it ran out of memory. It seems to me=20 > > > that with the cache turned off, frames should be rendered=20 > > > successively and not stored in the memory. > > > I have make some tests, it seems that PyMOL indeed loads=20 > all PDB but=20 > > > crashes just after the mpng command line. So, is the=20 > problem could=20 > > > be due to an error in my script? Or may be because my system is=20 > > > quite large (> 15000 atoms * > 1000 frames!). > > > Any suggestion will be welcome! > > >=20 > > > Nicolas > > >=20 > > > PS : congratulation to PyMOL authors! It's a=20 > well-conceived and well=20 > > > 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 > > > ------------------------------------------------------- > > > SF.Net email is Sponsored by the Better Software=20 > Conference & EXPO=20 > > > September 19-22, 2005 * San Francisco, CA * Development Lifecycle=20 > > > Practices Agile & Plan-Driven Development * Managing Projects &=20 > > > Teams * Testing & QA Security * Process Improvement &=20 > Measurement *=20 > > > http://www.sqe.com/bsce5sf=20 > > > _______________________________________________ > > > PyMOL-users mailing list > > > PyM...@li... > > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > >=20 > > >=20 > > >=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 >=20 |