pymol: Pymol crashes with segmentation fault

Charlie Kravetz cjk at teamcharliesangels.com
Thu Nov 13 14:12:00 UTC 2008


On Wed, 12 Nov 2008 12:44:53 -0600
"Khurrum Maqbool" <khurrum at cbse.uab.edu> wrote:

> Package: pymol
> Version: 1.1~beta3-3
> Severity: important
> 
> 
> When I run pymol in Ubuntu 8.10, I get a segmentation fault if I do
> the following:
> 
> 1. Go to Help > Pymol
> 2. Go to Plugin > Apbs tools > and click on any button for example
> Choose Externally Generated PQR, or Run APBS or any other button
> 
> I have tried version 0_99, 1, 1.1 and I also tried building from
> source ( svn co https://pymol.svn.sourceforge.net/svnroot/pymol
> pymol ) but I get the same exact problem.
> 
> I have tried this with Ubuntu 8.10 with nvidia quadro fx3700. nvidia
> geforce 7900, an ATI card but they all give the same problem.
> 
> However, we have other machines not running ubuntu 8.10 with python
> versions less than 2.5.1 and pymol works perfectly on those.
> 
> Is there anything else I can try and do you require any extra
> information?
> 
> The following is a gdb output:
> 
> GNU gdb 6.8-debian
> Copyright (C) 2008 Free Software Foundation, Inc.
> License GPLv3+: GNU GPL version 3 or later
> <http://gnu.org/licenses/gpl.html> This is free software: you are
> free to change and redistribute it. There is NO WARRANTY, to the
> extent permitted by law.  Type "show copying" and "show warranty" for
> details. This GDB was configured as "i486-linux-gnu"...
> (no debugging symbols found)
> (gdb) r /usr/lib/python2.5/site-packages/pymol/__init__.py
> Starting
> program: /usr/bin/python /usr/lib/python2.5/site-packages/pymol/__init__.py
> (no debugging symbols found) (no debugging symbols found)
> (no debugging symbols found)
> [Thread debugging using libthread_db enabled]
> (no debugging symbols found)
> (no debugging symbols found)
> (no debugging symbols found)
> (no debugging symbols found)
> [New Thread 0xb7d798c0 (LWP 17065)]
> (no debugging symbols found)
> (no debugging symbols found)
> (no debugging symbols found)
> (no debugging symbols found)
>  PyMOL(TM) Molecular Graphics System, Version 1.2b0pre.
>  Copyright (C) 2008 by DeLano Scientific LLC.
>  All Rights Reserved.
> 
>     Created by Warren L. DeLano, Ph.D.
> 
>     Other Major Authors and Contributors:
> 
>        Ralf W. Grosse-Kunstleve, 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: NVIDIA Corporation
>   GL_RENDERER: GeForce 7900 GS/PCI/SSE2
>   GL_VERSION: 2.1.2 NVIDIA 177.80
> [New Thread 0xb4ee0b90 (LWP 17068)]
> [New Thread 0xb46dfb90 (LWP 17069)]
>  Adapting to GeForce hardware.
>  Detected 2 CPU cores.  Enabled multithreaded rendering.
> [New Thread 0xb3c84b90 (LWP 17085)]
> [Thread 0xb3c84b90 (LWP 17085) exited]
> 
> Program received signal SIGSEGV, Segmentation fault.
> [Switching to Thread 0xb46dfb90 (LWP 17069)]
> 0x00000000 in ?? ()
> (gdb) quit
> 
> 
> The following is output from 'bt full'
> 
> Program received signal SIGSEGV, Segmentation fault.
> [Switching to Thread 0xb4722b90 (LWP 17866)]
> 0x00000000 in ?? ()
> (gdb) bt full
> #0  0x00000000 in ?? ()
> No symbol table info available.
> #1  0xb5149385 in ?? () from /usr/lib/libBLT.2.4.so.8.4
> No symbol table info available.
> #2  0xb51495a0 in ?? () from /usr/lib/libBLT.2.4.so.8.4
> No symbol table info available.
> #3  0xb4f5d5ce in TclInvokeStringCommand ()
> from /usr/lib/libtcl8.4.so.0 No symbol table info available.
> #4  0xb4f5e94e in TclEvalObjvInternal () from /usr/lib/libtcl8.4.so.0
> No symbol table info available.
> #5  0xb4f5ec10 in Tcl_EvalObjv () from /usr/lib/libtcl8.4.so.0
> No symbol table info available.
> #6  0xb51eca1d in ?? ()
> from /usr/lib/python2.5/lib-dynload/_tkinter.so No symbol table info
> available. #7  0x080cea39 in PyEval_EvalFrameEx ()
> No symbol table info available.
> #8  0x080d0345 in PyEval_EvalCodeEx ()
> No symbol table info available.
> #9  0x080ce728 in PyEval_EvalFrameEx ()
> No symbol table info available.
> #10 0x080cfbf5 in PyEval_EvalFrameEx ()
> No symbol table info available.
> #11 0x080d0345 in PyEval_EvalCodeEx ()
> ---Type <return> to continue, or q <return> to quit---
> No symbol table info available.
> #12 0x080ce728 in PyEval_EvalFrameEx ()
> No symbol table info available.
> #13 0x080cfbf5 in PyEval_EvalFrameEx ()
> No symbol table info available.
> #14 0x080d0345 in PyEval_EvalCodeEx ()
> No symbol table info available.
> #15 0x08117891 in ?? ()
> No symbol table info available.
> #16 0x0805d867 in PyObject_Call ()
> No symbol table info available.
> #17 0x080c850c in PyEval_CallObjectWithKeywords ()
> No symbol table info available.
> #18 0x080c7ed4 in ?? ()
> No symbol table info available.
> #19 0x080cea39 in PyEval_EvalFrameEx ()
> No symbol table info available.
> #20 0x080d0345 in PyEval_EvalCodeEx ()
> No symbol table info available.
> #21 0x08117891 in ?? ()
> No symbol table info available.
> #22 0x0805d867 in PyObject_Call ()
> No symbol table info available.
> ---Type <return> to continue, or q <return> to quit---
> #23 0x08063a7a in ?? ()
> No symbol table info available.
> #24 0x0805d867 in PyObject_Call ()
> No symbol table info available.
> #25 0x080c850c in PyEval_CallObjectWithKeywords ()
> No symbol table info available.
> #26 0xb51ea097 in ?? ()
> from /usr/lib/python2.5/lib-dynload/_tkinter.so No symbol table info
> available. #27 0xb4f5d5ce in TclInvokeStringCommand ()
> from /usr/lib/libtcl8.4.so.0 No symbol table info available.
> #28 0xb4f5e94e in TclEvalObjvInternal () from /usr/lib/libtcl8.4.so.0
> No symbol table info available.
> #29 0xb4f8ad71 in ?? () from /usr/lib/libtcl8.4.so.0
> No symbol table info available.
> #30 0xb4f88db8 in TclCompEvalObj () from /usr/lib/libtcl8.4.so.0
> No symbol table info available.
> #31 0xb4f5fc24 in Tcl_EvalObjEx () from /usr/lib/libtcl8.4.so.0
> No symbol table info available.
> #32 0xb504eea0 in TkInvokeMenu () from /usr/lib/libtk8.4.so.0
> No symbol table info available.
> #33 0xb504ea76 in ?? () from /usr/lib/libtk8.4.so.0
> No symbol table info available.
> #34 0xb4f5e94e in TclEvalObjvInternal () from /usr/lib/libtcl8.4.so.0
> ---Type <return> to continue, or q <return> to quit---
> No symbol table info available.
> #35 0xb4f5ec10 in Tcl_EvalObjv () from /usr/lib/libtcl8.4.so.0
> No symbol table info available.
> #36 0xb4f5fd6b in Tcl_EvalObjEx () from /usr/lib/libtcl8.4.so.0
> No symbol table info available.
> #37 0xb4fc0af6 in Tcl_UplevelObjCmd () from /usr/lib/libtcl8.4.so.0
> No symbol table info available.
> #38 0xb4f5e94e in TclEvalObjvInternal () from /usr/lib/libtcl8.4.so.0
> No symbol table info available.
> #39 0xb4f8ad71 in ?? () from /usr/lib/libtcl8.4.so.0
> No symbol table info available.
> #40 0xb4f88db8 in TclCompEvalObj () from /usr/lib/libtcl8.4.so.0
> No symbol table info available.
> #41 0xb4fc107e in TclObjInterpProc () from /usr/lib/libtcl8.4.so.0
> No symbol table info available.
> #42 0xb4f5e94e in TclEvalObjvInternal () from /usr/lib/libtcl8.4.so.0
> No symbol table info available.
> #43 0xb4f5f812 in Tcl_EvalEx () from /usr/lib/libtcl8.4.so.0
> No symbol table info available.
> #44 0xb500e989 in Tk_BindEvent () from /usr/lib/libtk8.4.so.0
> No symbol table info available.
> #45 0xb50152c7 in TkBindEventProc () from /usr/lib/libtk8.4.so.0
> No symbol table info available.
> ---Type <return> to continue, or q <return> to quit---
> #46 0xb501ddc9 in Tk_HandleEvent () from /usr/lib/libtk8.4.so.0
> No symbol table info available.
> #47 0xb501e628 in ?? () from /usr/lib/libtk8.4.so.0
> No symbol table info available.
> #48 0xb4fb53eb in Tcl_ServiceEvent () from /usr/lib/libtcl8.4.so.0
> No symbol table info available.
> #49 0xb4fb5719 in Tcl_DoOneEvent () from /usr/lib/libtcl8.4.so.0
> No symbol table info available.
> #50 0xb51e7f01 in ?? ()
> from /usr/lib/python2.5/lib-dynload/_tkinter.so No symbol table info
> available. #51 0x080cea39 in PyEval_EvalFrameEx ()
> No symbol table info available.
> #52 0x080d0345 in PyEval_EvalCodeEx ()
> No symbol table info available.
> #53 0x080ce728 in PyEval_EvalFrameEx ()
> No symbol table info available.
> #54 0x080d0345 in PyEval_EvalCodeEx ()
> No symbol table info available.
> #55 0x080ce728 in PyEval_EvalFrameEx ()
> No symbol table info available.
> #56 0x080d0345 in PyEval_EvalCodeEx ()
> No symbol table info available.
> #57 0x0811797e in ?? ()
> ---Type <return> to continue, or q <return> to quit---
> No symbol table info available.
> #58 0x0805d867 in PyObject_Call ()
> No symbol table info available.
> #59 0x080cd502 in PyEval_EvalFrameEx ()
> No symbol table info available.
> #60 0x080cfbf5 in PyEval_EvalFrameEx ()
> No symbol table info available.
> #61 0x080cfbf5 in PyEval_EvalFrameEx ()
> No symbol table info available.
> #62 0x080d0345 in PyEval_EvalCodeEx ()
> No symbol table info available.
> #63 0x08117891 in ?? ()
> No symbol table info available.
> #64 0x0805d867 in PyObject_Call ()
> No symbol table info available.
> #65 0x08063a7a in ?? ()
> No symbol table info available.
> #66 0x0805d867 in PyObject_Call ()
> No symbol table info available.
> #67 0x080c850c in PyEval_CallObjectWithKeywords ()
> No symbol table info available.
> #68 0x080f9e68 in ?? ()
> No symbol table info available.
> ---Type <return> to continue, or q <return> to quit---
> #69 0xb7f5250f in start_thread ()
> from /lib/tls/i686/cmov/libpthread.so.0 No symbol table info
> available. #70 0xb7ea07ee in clone ()
> from /lib/tls/i686/cmov/libc.so.6 No symbol table info available.
> 
> 
> -- System Information:
> Debian Release: lenny/sid
>   APT prefers intrepid-updates
>   APT policy: (500, 'intrepid-updates'), (500, 'intrepid-security'),
> (500, 'intrepid') Architecture: i386 (i686)
> 
> Kernel: Linux 2.6.24-19-generic (SMP w/2 CPU cores)
> Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
> Shell: /bin/sh linked to /bin/dash
> 
> Versions of packages pymol depends on:
> ii  freeglut3       2.4.0-6.1                OpenGL Utility Toolkit
> ii  libc6           2.8~20080505-0ubuntu7    GNU C Library: Shared
> libraries ii  libfreetype6    2.3.7-2ubuntu1           FreeType 2
> font engine, shared lib ii  libgcc1         1:4.3.2-1ubuntu11
> GCC support library ii  libgl1-mesa-glx 7.2-1ubuntu2             A
> free implementation of the OpenG ii  libglu1-mesa [l
> 7.2-1ubuntu2             The OpenGL utility library (GLU) ii
> libpng12-0      1.2.27-1                 PNG library - runtime ii
> libstdc++6      4.3.2-1ubuntu11          The GNU Standard C++ Library
> v3 ii  python          2.5.2-1ubuntu1           An interactive
> high-level object-o ii  python-pmw      1.3.2-3                  Pmw
> -- Python MegaWidgets ii  python-support  0.8.4
> automated rebuilding support for P ii  python-tk
> 2.5.2-1ubuntu1           Tkinter - Writing Tk applications ii
> zlib1g          1:1.2.3.3.dfsg-12ubuntu1 compression library - runtime
> 
> Versions of packages pymol recommends:
> ii  apbs                          1.0.0-2    Adaptive Poisson
> Boltzmann Solver
> 
> -- no debconf information
> 

Can you file this on launchpad? I know the system sent it to the users
mailing list, but it never gets worked if it stays here. 

The right place to file bug reports is:
https://bugs.launchpad.net/ubuntu

That will give the developers a chance to see if they can fix it.

Thanks.

-- 
Charlie Kravetz 
Linux Registered User Number 425914          [http://counter.li.org/]
Never let anyone steal your DREAM.           [http://keepingdreams.com]




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