Hi, Sorry, this was not compiled properly! catchsegv showed that tcl/tk 8.6 was being used. Setting LD_LIBRARY_PATH for the alternative tcl/tk libraries for the Python and PyMOL compilation fixed the problem. The segfault is gone when using Python 2.5.5 with tcl/tk 8.5. It also works with Python 2.6.5 with tcl/tk 8.5. So the problem looks like it is triggered by the new tck/tk 8.6 libraries.
Regards, Edward On 10 June 2010 17:46, Edward d'Auvergne <edward.dauver...@gmail.com> wrote: > Hi, > > I have a similar problem to Ben in this post: > > http://sourceforge.net/mailarchive/message.php?msg_id=20100512182803.GA21563%40crystal.harvard.edu > > I am using the svn r3910 with various versions of python and tcl/tk. > I see the following message: > > IRQ's not enabled, falling back to busy waits: 2 0 > PyMOL(TM) Molecular Graphics System, Version 1.3. > Copyright (c) Schrodinger, LLC. > All Rights Reserved. > > Created by Warren L. DeLano, Ph.D. > > PyMOL is user-supported open-source software. Although some versions > are freely available, PyMOL is not in the public domain. > > If PyMOL is helpful in your work or study, then please volunteer > support for our ongoing efforts to create open and affordable scientific > software by purchasing a PyMOL Maintenance and/or Support subscription. > > More information can be found at "http://www.pymol.org";. > > Enter "help" for a list of commands. > Enter "help <command-name>" for information on a specific command. > > Hit ESC anytime to toggle between text and graphics. > > OpenGL graphics engine: > GL_VENDOR: Advanced Micro Devices, Inc. > GL_RENDERER: Mesa DRI R600 (RV635 9598) 20090101 TCL > GL_VERSION: 2.0 Mesa 7.8.1 > Detected 2 CPU cores. Enabled multithreaded rendering. > ./pymol: line 2: 7161 Segmentation fault > /media/disk/bin/python2.5 > /media/disk/lib/python2.5/site-packages/pymol/__init__.py "$@" > > This specific message is with: > > pymol: r3910 > python: 2.5.5 > tck/tk: 8.5.8 > pmw: 1.3.2 > GPU: dual head "ATI Radeon HD 2000 and later (radeon/fglrx)" GPU > driver: radeon (x11-driver-video-ati) > OS: Mandriva 2010 spring (rc2) > > Is this a known issue? Is there a way of disabling multithreaded > rendering for testing this? Some conspicuous dmseg messages are: > > python2.5[8829]: segfault at 0 ip (null) sp 00007fff00eabee8 error 14 > in python2.5[400000+11c000] > python2.5[8846]: segfault at 0 ip (null) sp 00007fffd0c51f68 error 14 > in python2.5[400000+11c000] > python2.5[8871]: segfault at 0 ip (null) sp 00007fff515419c8 error 14 > in python2.5[400000+11c000] > python2.5[9051]: segfault at 0 ip (null) sp 00007fffba96bda8 error 14 > in python2.5[400000+11c000] > python2.5[9198]: segfault at 0 ip (null) sp 00007fff56bf19d8 error 14 > in python2.5[400000+11c000] > [drm] Resetting GPU > [drm] Resetting GPU > python2.5[2825]: segfault at 8 ip 00007f090d03e626 sp 00007f08f5701e30 > error 4 in libX11.so.6.3.0[7f090cfec000+134000] > python2.5[5640]: segfault at 8 ip 00007f6403be9626 sp 00007f63ec43de30 > error 4 in libX11.so.6.3.0[7f6403b97000+134000] > python2.5[7168]: segfault at 8 ip 00007f07fb138626 sp 00007f07e37fbe30 > error 4 in libX11.so.6.3.0[7f07fb0e6000+134000] > python2.5[8252]: segfault at 8 ip 00007fb3d38ae626 sp 00007fb3bbf71e30 > error 4 in libX11.so.6.3.0[7fb3d385c000+134000] > python2.5[8302]: segfault at 8 ip 00007f00abd88626 sp 00007f009444be30 > error 4 in libX11.so.6.3.0[7f00abd36000+134000] > > Cheers, > > Edward > ------------------------------------------------------------------------------ ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
