VMD-L Mailing List

From: Tru Huynh (tru_at_pasteur.fr)
Date: Thu Dec 13 2012 - 11:41:46 CST

On Tue, Dec 11, 2012 at 08:59:37AM -0600, John Stone wrote:
> Tru,
> What happens if you run VMD like this:
> vmd -debug
>
> Type "run" at the gdb prompt. When it crashes, type "where"
> and report the results back here.
>
[tru_at_yippy ~]$ vmd -debug
***
*** Running VMD in debugger, type 'run' at debugger prompt
***
GNU gdb (GDB) CentOS (7.0.1-42.el5.centos.1)
Copyright (C) 2009 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 /c5/shared/vmd/vmd-1.9.1/vmd_LINUXAMD64...(no debugging symbols found)...done.
(gdb) run
Starting program: /c5/shared/vmd/vmd-1.9.1/vmd_LINUXAMD64
warning: no loadable sections found in added symbol-file system-supplied DSO at 0x2aaaaaaab000
[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, 16 CPUs detected.
Info) Free system memory: 128549MB (99%)
Info) Creating CUDA device pool and initializing hardware...
[New Thread 0x40a00940 (LWP 12129)]
[New Thread 0x41401940 (LWP 12130)]
[New Thread 0x41e02940 (LWP 12131)]
[New Thread 0x42803940 (LWP 12132)]
[New Thread 0x43204940 (LWP 12133)]
[New Thread 0x43c05940 (LWP 12134)]
[New Thread 0x44606940 (LWP 12135)]
[New Thread 0x45007940 (LWP 12136)]
CUDA error: invalid device symbol, CUDAClearDevice.cu line 62
CUDA error: invalid device symbol, CUDAClearDevice.cu line 62
CUDA error: invalid device symbol, CUDAClearDevice.cu line 62
CUDA error: invalid device symbol, CUDAClearDevice.cu line 62
Info) Detected 4 available CUDA accelerators:
Info) [0] GeForce GTX 680 8 SM_3.0 @ 1.14 GHz, 4.0GB RAM, OIO, ZCP
Info) [1] GeForce GTX 680 8 SM_3.0 @ 1.14 GHz, 4.0GB RAM, OIO, ZCP
Info) [2] GeForce GTX 680 8 SM_3.0 @ 1.14 GHz, 4.0GB RAM, OIO, ZCP
Info) [3] GeForce GTX 680 8 SM_3.0 @ 1.14 GHz, 4.0GB RAM, OIO, ZCP
Warning) Detected X11 'Composite' extension: if incorrect display occurs
Warning) try disabling this optional X server feature.
Info) OpenGL renderer: GeForce 210/PCI/SSE2
Info) Features: STENCIL MSAA(4) MDE MTX NPOT PP PS GLSL(OVFG)
XRequest.143: BadLength (poly request too large or internal Xlib length error) 0x2200046
Warning) GPU driver failed to compile shader:
Warning) /c5/shared/vmd/vmd-1.9.1/shaders/vmd
Warning) This GPU/driver is buggy, or doesn't fully implement GLSL.
Warning) Set environment variable VMDGLSLVERBOSE for more info.
Info) GLSL rendering mode is NOT available.
Info) Textures: 2-D (8192x8192), 3-D (2048x2048x2048), Multitexture (4)

Program received signal SIGSEGV, Segmentation fault.
0x0000000000a934b4 in __intel_ssse3_rep_memcpy ()
(gdb) where
#0 0x0000000000a934b4 in __intel_ssse3_rep_memcpy ()
#1 0x0000000000a8ae86 in _intel_fast_memcpy.P ()
#2 0x00000000005fe9ed in PluginMgr::register_cb(void*, vmdplugin_t*) ()
#3 0x00000000009b0103 in molfile_babelplugin_register ()
#4 0x00000000005fe0fb in PluginMgr::load_static_plugins() ()
#5 0x000000000065e493 in VMDApp::VMDinit(int, char**, char const*, int*, int*)
    ()
#6 0x000000000068729d in main ()
(gdb)

Cheers,

Tru 

-- 
Dr Tru Huynh          | http://www.pasteur.fr/recherche/unites/Binfs/
mailto:tru_at_pasteur.fr | tel/fax +33 1 45 68 87 37/19
Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France