From: Neil R. <n.a...@le...> - 2006-09-28 08:16:17
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Dear All, Has anyone come across issues running PyMOL on suse linux 10.0? I have just 'upgraded' from Windows, and am running: Suse Linux 10.0 Dual Opteron 275, 4Gb RAM Nvidia 6600GT KDE version: 3.4.2 Level "b" 2.6.13-15.12-smp x86_64 and am having real problems. I have tried 0.99 rc6 and rc7, and the 1.00 beta 01 that is described as "for testing on 64-bit linux", all with the same result. PyMOL appears to start normally OpenGL graphics engine: GL_VENDOR: NVIDIA Corporation GL_RENDERER: unknown board/PCI/SSE2 GL_VERSION: 2.1.0 NVIDIA 96.25 Detected 4 CPUs. Enabled multithreaded rendering. But as soon any object (either ccp4 map or coordinates) is read in, the whole machine irretrievably crashes. Any suggestions would be much appreciated as we are stumped. We are about to try different OpenGL / nvidia driver combinations but I thought I'd see if anyone else had had similar experiences so far. Everything else about the machine is rock-solid and stable, including the latest build of Chimera that is running exceptionally well. Best regards, Neil Ranson |
From: Peter A. M. <pa...@co...> - 2006-09-28 13:06:28
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Hi, > I have tried 0.99 rc6 and rc7, and the 1.00 beta 01 that is described as > "for testing on 64-bit linux", all with the same result. PyMOL appears > to start normally Good troubleshooting procedure....I've had no problems w\ 0.99rc9 on suse 10.0 (single cpu though...so smp/threading issues would be a place to look). One thing you don't mention is if you're using the binary or source version (trying both shouldn't make a difference, but is straightfoward enough that it's worth checking). > But as soon any object (either ccp4 map or coordinates) is read in, the > whole machine irretrievably crashes. Could you provide more details on how it crashes (exceptions, core dumps, x-windows freeze, machine catches fire)? > Any suggestions would be much appreciated as we are stumped. We are > about to try different OpenGL / nvidia driver combinations but I thought > I'd see if anyone else had had similar experiences so far. I was having sporadic issues a few months back with pymol sporadically freezing the x-server (and ending up with a process that would refuse to stop, even when killed by root); is this what you mean by the whole machine crashing? If so, check the list archive for details (the short version is that it could be caused by issues w\ binary graphics card drivers, and a possible fix is to use the open source drivers). Good luck, Pete Pete Meyer Fu Lab BMCB grad student Cornell University |
From: Neil R. <n.a...@le...> - 2006-09-28 14:52:00
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Thanks for the reply. "Irretrievably crashing" means that everything stops dead. The screen freezes, mouse/keyboard become unresponsive, the machine becomes unreachable (via ssh or even ping) from other workstations. Background processes instantaneously halt. A 'proper' crash in other words! Cheers, Neil. |
From: Peter A. M. <pa...@co...> - 2006-09-28 18:31:50
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> Thanks for the reply. "Irretrievably crashing" means that everything stops dead. The screen freezes, mouse/keyboard become unresponsive, the machine becomes unreachable (via ssh or even ping) from other > workstations. Background processes instantaneously halt. A 'proper' crash in other words! It does sound like an impressive crash. One things that sometimes works for me in cases like that is to have an open ssh session running from another machine running top (you've probably tried this already). It won't fix anything, but occaisonally helps figure out what the problem is. One option would be to try running through a stack of live-cd's of different distributions (boot, try to launch pymol and see if it freezes, and repeat). Again, this is more to figure out where the problem is than to fix it. Most likely it's something with the graphics drivers, but if chimera works alright then I'd keep an open mind as to what could be causing the problem (presumably they're both using the same opengl and x-windows drivers). Your best bet is probably to try out the different driver versions you were talking about (my normal approach would be to keep recompiling with as many options disabled as possible...no smp, multi-threading, shared libraries; but that would take some patience when the system freezes every time you get it wrong). Good luck, Pete Pete Meyer Fu Lab BMCB grad student Cornell University |