From: Michael W. <weberm@Staff.Uni-Marburg.DE> - 2009-01-16 12:56:06
|
Hi, I have a problem when trying to ray 750,750 a quite large ribosome file with maximum quality. Size of the relevant PyMOL v1.1 file is 100 MB (or 31 MB after reducing objects I do not need for the figure production). PyMOL simply crashes under Windows Vista Home Premium as well as under Ubuntu Linux v8.04 LTS without error report. My dual OS system is a Samsung Aura Seven Notebook (Core2Duo @2.4 GHz each, 3 GB of RAM, NVIDIA GeForce 9200M GS graphics board with 256 MB of RAM, 12" TFT @1280x800 resolution settings). I first thought the RAM under Vista is still insufficient (Vista alone takes 900 MB of the 3 GB of memory) but then I realized that this crash occurs as well under Linux. However, since both OS are 32 bit and therefore to my (limited) knowledge cannot handle more than 2 GB in a single task, RAM limitation might still be an issue to think about, right? I have experienced (and occasionally reported) this type of serious crashes with PyMOL on a broad variety of machines over some years now - usually occurring when trying to render final files - but, sadly, none of these has ever been diagnosed and fixed properly. Maybe this time I am lucky and someone knows what to do? Best regards, Michael. |
From: Schubert, C. [PRDUS] <CSC...@it...> - 2009-01-16 13:12:09
|
Michael, play around with the hash_max value, which seem to partially control how much memory is used during rendering. You can also reduce the quality of the rendering Display->Quality, that should reduce memory requirements too. I know you don't want that, but do you really need max quality? Finally on Unix or even Windoze you can look at how much memory is consumed during rendering using top (on Unix) and the task manager on windows. That should give you some clue if you are really exceeding the physical memory or not. Finally you could split the rendering into smaller pieces, export to Povray, combine the files under a common header and render there, alternatively try if the "Draw" command gives you what you want, albeit not quite as fancy as the raytracer. HTH Carsten -----Original Message----- From: Michael Weber [mailto:weberm@Staff.Uni-Marburg.DE] Sent: Friday, January 16, 2009 7:24 AM To: pym...@li... Subject: [PyMOL] PyMOL crashes under Vista Home Premium & Ubuntu 8.04 LTS Hi, I have a problem when trying to ray 750,750 a quite large ribosome file with maximum quality. Size of the relevant PyMOL v1.1 file is 100 MB (or 31 MB after reducing objects I do not need for the figure production). PyMOL simply crashes under Windows Vista Home Premium as well as under Ubuntu Linux v8.04 LTS without error report. My dual OS system is a Samsung Aura Seven Notebook (Core2Duo @2.4 GHz each, 3 GB of RAM, NVIDIA GeForce 9200M GS graphics board with 256 MB of RAM, 12" TFT @1280x800 resolution settings). I first thought the RAM under Vista is still insufficient (Vista alone takes 900 MB of the 3 GB of memory) but then I realized that this crash occurs as well under Linux. However, since both OS are 32 bit and therefore to my (limited) knowledge cannot handle more than 2 GB in a single task, RAM limitation might still be an issue to think about, right? I have experienced (and occasionally reported) this type of serious crashes with PyMOL on a broad variety of machines over some years now - usually occurring when trying to render final files - but, sadly, none of these has ever been diagnosed and fixed properly. Maybe this time I am lucky and someone knows what to do? Best regards, Michael. ------------------------------------------------------------------------------ This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword _______________________________________________ PyMOL-users mailing list PyM...@li... https://lists.sourceforge.net/lists/listinfo/pymol-users |
From: Pete M. <pa...@mc...> - 2009-01-16 15:44:02
|
> with maximum quality. Size of the relevant PyMOL v1.1 file is 100 MB (or > 31 MB after reducing objects I do not need for the figure production). If lack of memory is the problem, try loading your scene manually or through a script instead of using a session file. For reasons I don't recall at the moment, pymol uses more memory with a pse file than with the same objects loaded through a script (you could check the list archives for more details if you're curious). > PyMOL simply crashes under Windows Vista Home Premium as well as under > Ubuntu Linux v8.04 LTS without error report. My dual OS system is a Not sure about windows, but with linux you should get some level of messages by launching from a command prompt instead of an icon. If you're running out of memory, you'll get a core dump message (at least, that the usual symptom on my systems. > both OS are 32 bit and therefore to my (limited) knowledge cannot handle > more than 2 GB in a single task, RAM limitation might still be an issue You might want to have top running in a different terminal so watch how much memory pymol is trying to use (or is able to use before crashing). |
From: H. A. S. <ad...@st...> - 2009-01-16 16:02:37
|
One of my tricks is to only show part of the structure at a time, ray each part individually and the reassemble them in Photoshop. I do this all the time with the huge multi protein PyMol sessions I have to work on. It depends on your orientation in the viewer though, be careful to not cut anything off. With the ribo you can hide the large or the small subunit, render each separately, and then reassemble. Michael Weber wrote: > Hi, > I have a problem when trying to ray 750,750 a quite large ribosome file > with maximum quality. Size of the relevant PyMOL v1.1 file is 100 MB (or > 31 MB after reducing objects I do not need for the figure production). > PyMOL simply crashes under Windows Vista Home Premium as well as under > Ubuntu Linux v8.04 LTS without error report. My dual OS system is a > Samsung Aura Seven Notebook (Core2Duo @2.4 GHz each, 3 GB of RAM, NVIDIA > GeForce 9200M GS graphics board with 256 MB of RAM, 12" TFT @1280x800 > resolution settings). I first thought the RAM under Vista is still > insufficient (Vista alone takes 900 MB of the 3 GB of memory) but then > I realized that this crash occurs as well under Linux. However, since > both OS are 32 bit and therefore to my (limited) knowledge cannot handle > more than 2 GB in a single task, RAM limitation might still be an issue > to think about, right? > I have experienced (and occasionally reported) this type of serious > crashes with PyMOL on a broad variety of machines over some years now - > usually occurring when trying to render final files - but, sadly, none > of these has ever been diagnosed and fixed properly. Maybe this time I > am lucky and someone knows what to do? > Best regards, > Michael. > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by: > SourcForge Community > SourceForge wants to tell your story. > http://p.sf.net/sfu/sf-spreadtheword > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > -- _______________________________________ H. Adam Steinberg Artist, Scientist <http://adam.steinbergs.us> Information Technology and Media Center Department of Biochemistry University of Wisconsin-Madison 433 Babcock Drive Madison, WI 53706 608/265-4982 _______________________________________ |