VMD-L Mailing List

From: Burlen Loring (burlen.loring_at_gmail.com)
Date: Tue Mar 31 2015 - 16:20:44 CDT

Hi ,

I am having some issue with vmd 1.9.2. As soon as I open a file (the
first example in the tutorial) there is a crash. I am pasting a stack
trace and the output below when running: vmd -debug. First I tried the
binary from the vmd site, then I tried building form source, but the
crash is the same. Any idea what is going wrong here?

Thanks
Burlen

$vmd -debug
***
*** Running VMD in debugger, type 'run' at debugger prompt
***
GNU gdb (GDB) Red Hat Enterprise Linux (7.0.1-23.el5_5.1)
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
/global/common/carver/graphics/vmd/1.9.2/lib/vmd/vmd_LINUXAMD64...done.
(gdb) run
Starting program:
/global/common/carver/graphics/vmd/1.9.2/lib/vmd/vmd_LINUXAMD64
[Thread debugging using libthread_db enabled]
[New Thread 0x50000940 (LWP 26008)]
Info) VMD for LINUXAMD64, version 1.9.2 (February 19, 2015)
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, 8 CPUs detected.
Info) Free system memory: 38022MB (78%)
Info) OpenGL renderer: Mesa GLX Indirect
Info) Features: STENCIL MDE MTX PP PS
Info) GLSL rendering mode is NOT available.
Info) Textures: 2-D (2048x2048), Multitexture (8)
vmd > Info) Using plugin pdb for structure file
/global/common/carver/graphics/vmd/tutorial/1ubq.pdb
Info) Using plugin pdb for coordinates from file
/global/common/carver/graphics/vmd/tutorial/1ubq.pdb
Info) Determining bond structure from distance search ...
[New Thread 0x60001940 (LWP 26018)]
[New Thread 0x70002940 (LWP 26019)]
[Thread 0x70002940 (LWP 26019) exited]
[New Thread 0x7fffe2fc4940 (LWP 26020)]
[Thread 0x60001940 (LWP 26018) exited]
[Thread 0x7fffe2fc4940 (LWP 26020) exited]
[New Thread 0x7fffd2fc3940 (LWP 26021)]
[Thread 0x7fffd2fc3940 (LWP 26021) exited]
[New Thread 0x7fffc2fc2940 (LWP 26022)]
[New Thread 0x7fffb2fc1940 (LWP 26023)]
[Thread 0x7fffc2fc2940 (LWP 26022) exited]
[Thread 0x7fffb2fc1940 (LWP 26023) exited]

Program received signal SIGSEGV, Segmentation fault.
0x00007fffef3c8a38 in pthread_join () from /lib64/libpthread.so.0
(gdb) where
#0 0x00007fffef3c8a38 in pthread_join () from /lib64/libpthread.so.0
#1 0x00000000004c2a18 in vmd_bondsearch_thr(float const*, float const*,
GridSearchPairlist*, int, int**, int*, int**, int, float) ()
#2 0x000000004011eb85 in ?? ()
#3 0x0000000000000000 in ?? ()
(gdb)