[Bug 297699] [NEW] Pymol crashes with segmentation fault

garg khurrum1 at gmail.com
Thu Nov 13 15:38:24 UTC 2008 

Public bug reported:

Binary package hint: pymol

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

** Affects: pymol (Ubuntu)
     Importance: Undecided
         Status: New

-- 
Pymol crashes with segmentation fault
https://bugs.launchpad.net/bugs/297699
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