VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Apr 01 2015 - 09:51:15 CDT

Burlen,
  This is helpful. What version of Linux is on the system you're using,
and which of the 64-bit VMD Linux packages did you install? I'm particularly
interested in the output of these commands:
  uname -a
  cat /etc/issue

Cheers,
  John

On Wed, Apr 01, 2015 at 01:23:28AM -0700, Burlen Loring wrote:
> Hi John,
>
> Thanks for the help! So I tried text mode as you suggest but the
> crash is the same (output below).
>
> Although the OpenGL window pops up and I can interact with it there
> may be some OpenGL issue. I'll have to inquire as to the hardware
> etc. glxinfo command is not installed. This is a cluster, the login
> nodes may have some crappy graphics cards, folks are using it with
> NX, and I think this is the source of GLX Indirect. I'm pretty sure
> that vmd was running here at some point in the past. Again I'll have
> to ask the guy I'm taking over for ;-)
>
> Burlen
>
> $vmd -dispdev text
> 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: 38998MB (80%)
>
> vmd > mol new 1ubq.pdb
> Info) Using plugin pdb for structure file 1ubq.pdb
> Info) Using plugin pdb for coordinates from file 1ubq.pdb
> Info) Determining bond structure from distance search ...
> Segmentation fault
>
> On 3/31/2015 5:56 PM, John Stone wrote:
> >Hi,
> > From the logs you sent, I noticed this, which is a bit of a red flag:
> >Info) OpenGL renderer: Mesa GLX Indirect
> >What graphics hardware do you have in this machine?
> >
> >If you run VMD in text mode, and load the same file, do you have
> >the same seg fault? Run VMD in text mode like this:
> > vmd -dispdev text
> >
> >If you do NOT have the seg fault in this case, then I am assuming
> >problems with the OpenGL graphics configuration. On the other hand,
> >if you do encounter a seg fault here when running in text mode, then
> >we will need to dig into this in much more detail.
> >
> >If you can run the text mode test and get back to me, that'd be great.
> >
> >Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >
> >On Tue, Mar 31, 2015 at 02:20:44PM -0700, Burlen Loring wrote:
> >>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) 

-- 
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/