VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Aug 27 2013 - 11:31:32 CDT

Hi,
  This is likely caused by an incompatibility between Tk and your
SCIM international keyboard input scheme. Can you try disabling
your internationalized input mechanism and see if the problem goes away?

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Aug 26, 2013 at 01:33:57PM -0500, Yubo Fan wrote:
> Hello,
>
> VMD fails to run on Centos 6.4 with an error message "Segmentation fault
> (core dumped)". See below:
> [yubo_at_localhost IntIr5]$ vmd
> Info) VMD for LINUXAMD64, version 1.9.1 (February 1, 2012)
> Info) http://www.ks.uiuc.edu/Research/vmd/
> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> Info) Please include this reference in published work using VMD:
> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> Info) -------------------------------------------------------------
> Info) Multithreading available, 2 CPUs detected.
> Info) Free system memory: 7252MB (92%)
> Info) Creating CUDA device pool and initializing hardware...
> Info) Detected 1 available CUDA accelerator:
> Info) [0] Quadro FX 3800M 16 SM_1.1 @ 1.65 GHz, 1.0GB RAM, KTO, OIO,
> ZCP
> Warning) Detected X11 'Composite' extension: if incorrect display occurs
> Warning) try disabling this optional X server feature.
> Info) OpenGL renderer: Quadro FX 3800M/PCIe/SSE2
> Info) Features: STENCIL MSAA(16) MDE CVA MTX NPOT PP PS GLSL(OVFG)
> Info) Full GLSL rendering mode is available.
> Info) Textures: 2-D (8192x8192), 3-D (2048x2048x2048), Multitexture (4)
> Info) Detected 13 XInput devices, 1 usable device:
> Info) [8] Lid Switch, type: 261, classes: 0
> Info) Dynamically loaded 2 plugins in directory:
> Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
> Segmentation fault (core dumped)
> Then, VMD -debug was run to dig out possible problems. Under the debug
> shell, run and where were run with output listed below:
> [yubo_at_localhost IntIr5]$ vmd
> Info) VMD for LINUXAMD64, version 1.9.1 (February 1, 2012)
> Info) http://www.ks.uiuc.edu/Research/vmd/
> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> Info) Please include this reference in published work using VMD:
> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> Info) -------------------------------------------------------------
> Info) Multithreading available, 2 CPUs detected.
> Info) Free system memory: 7252MB (92%)
> Info) Creating CUDA device pool and initializing hardware...
> Info) Detected 1 available CUDA accelerator:
> Info) [0] Quadro FX 3800M 16 SM_1.1 @ 1.65 GHz, 1.0GB RAM, KTO, OIO,
> ZCP
> Warning) Detected X11 'Composite' extension: if incorrect display occurs
> Warning) try disabling this optional X server feature.
> Info) OpenGL renderer: Quadro FX 3800M/PCIe/SSE2
> Info) Features: STENCIL MSAA(16) MDE CVA MTX NPOT PP PS GLSL(OVFG)
> Info) Full GLSL rendering mode is available.
> Info) Textures: 2-D (8192x8192), 3-D (2048x2048x2048), Multitexture (4)
> Info) Detected 13 XInput devices, 1 usable device:
> Info) [8] Lid Switch, type: 261, classes: 0
> Info) Dynamically loaded 2 plugins in directory:
> Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
> Segmentation fault (core dumped)
> [yubo_at_localhost IntIr5]$ vmd -debug
> ***
> *** Running VMD in debugger, type 'run' at debugger prompt
> ***
> GNU gdb (GDB) Red Hat Enterprise Linux (7.2-60.el6_4.1)
> Copyright (C) 2010 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 "x86_64-redhat-linux-gnu".
> For bug reporting instructions, please see:
> <http://www.gnu.org/software/gdb/bugs/>...
> Reading symbols from /usr/local/lib/vmd/vmd_LINUXAMD64...(no debugging
> symbols found)...done.
> (gdb) run
> Starting program: /usr/local/lib/vmd/vmd_LINUXAMD64
> [Thread debugging using libthread_db enabled]
> Info) VMD for LINUXAMD64, version 1.9.1 (February 1, 2012)
> Info) http://www.ks.uiuc.edu/Research/vmd/
> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> Info) Please include this reference in published work using VMD:
> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> Info) -------------------------------------------------------------
> Info) Multithreading available, 2 CPUs detected.
> Info) Free system memory: 7051MB (89%)
> Info) Creating CUDA device pool and initializing hardware...
> [New Thread 0x7fffee8b2700 (LWP 6645)]
> [New Thread 0x7fffeddaf700 (LWP 6646)]
> Info) Detected 1 available CUDA accelerator:
> Info) [0] Quadro FX 3800M 16 SM_1.1 @ 1.65 GHz, 1.0GB RAM, KTO, OIO,
> ZCP
> Warning) Detected X11 'Composite' extension: if incorrect display occurs
> Warning) try disabling this optional X server feature.
> Info) OpenGL renderer: Quadro FX 3800M/PCIe/SSE2
> Info) Features: STENCIL MSAA(16) MDE CVA MTX NPOT PP PS GLSL(OVFG)
> Info) Full GLSL rendering mode is available.
> Info) Textures: 2-D (8192x8192), 3-D (2048x2048x2048), Multitexture (4)
> Info) Detected 13 XInput devices, 1 usable device:
> Info) [8] Lid Switch, type: 261, classes: 0
> Missing separate debuginfo for /usr/local/lib/vmd/libexpat.so.0
> Info) Dynamically loaded 2 plugins in directory:
> Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
>
> Program received signal SIGSEGV, Segmentation fault.
> 0x0000003fd8c503c6 in XGetICValues () from /usr/lib64/libX11.so.6
> Missing separate debuginfos, use: debuginfo-install
> glibc-2.12-1.107.el6_4.2.x86_64 libX11-1.5.0-4.el6.x86_64
> libXau-1.0.6-4.el6.x86_64 libXcursor-1.1.13-2.el6.x86_64
> libXext-1.3.1-2.el6.x86_64 libXfixes-5.0-3.el6.x86_64
> libXi-1.6.1-3.el6.x86_64 libXinerama-1.1.2-2.el6.x86_64
> libXrender-0.9.7-2.el6.x86_64 libgcc-4.4.7-3.el6.x86_64
> libselinux-2.0.94-5.3.el6_4.1.x86_64 libstdc++-4.4.7-3.el6.x86_64
> libxcb-1.8.1-1.el6.x86_64 mesa-libGLU-9.0-0.8.el6_4.3.x86_64
> zlib-1.2.3-29.el6.x86_64
> (gdb) where
> #0 0x0000003fd8c503c6 in XGetICValues () from /usr/lib64/libX11.so.6
> #1 0x00000000008d04fb in Tk_HandleEvent ()
> #2 0x00000000008d0e93 in ?? ()
> #3 0x0000000000964c0a in Tcl_ServiceEvent ()
> #4 0x0000000000964f87 in Tcl_DoOneEvent ()
> #5 0x00000000006a378b in TclTextInterp::doTkUpdate() ()
> #6 0x000000000064ca37 in UIText::check_event() ()
> #7 0x000000000052aff2 in CommandQueue::check_events() ()
> #8 0x000000000065d675 in VMDApp::VMDupdate(int) ()
> #9 0x0000000000687309 in main ()
>
> Would you please help to fix this problem?
>
> Thanks,
> Yubo 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/