Hi Edward, Choosing the correct Tcl/Tk version is necessary, and sometimes easy to overlook. Glad to hear it works.
Cheers, -- Jason On Thu, Jun 10, 2010 at 2:01 PM, Edward d'Auvergne <edw...@nmr-relax.com> wrote: > 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 > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ 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
