VMD-L Mailing List

From: Yubo Fan (pengpengtadie_at_gmail.com)
Date: Mon Aug 26 2013 - 13:33:57 CDT

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