VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Apr 01 2015 - 11:25:50 CDT

Axel,
  Yes, I completely agree.
That's why I've asked him to report the OS version...

Since he sees the problem when running in text mode, I think that the most
likely possibility is then a problem with their pthreads implementation,
particularly since he experienced the same problem with a version compiled
from source.

I just wanted to first eliminate broken OpenGL from the equation since
I've seen bad GL drivers corrupt memory and cause all kinds of side effects.

Cheers,
  John

On Wed, Apr 01, 2015 at 11:51:25AM -0400, Axel Kohlmeyer wrote:
> john,
>
> this looks similar to the threading bug that was in the Linux kernel
> on early RHEL 4.x versions.
> note that the program dies on joining the threads after the gridsearch
> for bonds. so i would doubt it is related to X11 or OpenGL.
>
> axel.
>
> On Wed, Apr 1, 2015 at 10:51 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
> > 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/
> >
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy. 

-- 
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/