From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Apr 01 2015 - 11:29:34 CDT

On Wed, Apr 1, 2015 at 12:25 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
> Axel,
> Yes, I completely agree.
> That's why I've asked him to report the OS version...

it has to be a rather old RHEL 5.x version. check out the debugger
version string that was quoted in the first e-mail:

GNU gdb (GDB) Red Hat Enterprise Linux (7.0.1-23.el5_5.1)

that looks like RHEL 5.1. debugger/compiler are usually updated
between RHEL updates, IIRC

axel.

>
> 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/

-- 
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.