VMD-L Mailing List

From: Burlen Loring (burlen.loring_at_gmail.com)
Date: Wed Apr 01 2015 - 12:09:34 CDT

Hi John,

Here is the result of issue and uname.

    Scientific Linux SL release 5.5 (Boron)
    Linux cvrsvc03 2.6.32-358.18.1.el6.nersc.x86_64 #1 SMP Wed Aug 28
    02:17:42 PDT 2013 x86_64 x86_64 x86_64 GNU/Linux

I also have the same segv on the newer system image, which is a login
option.

    Scientific Linux release 6.3 (Carbon)
    Linux cvrsvc03 2.6.32-358.18.1.el6.nersc.x86_64 #1 SMP Wed Aug 28
    02:17:42 PDT 2013 x86_64 x86_64 x86_64 GNU/Linux

The binary I tried is

    vmd-1.9.2.bin.LINUXAMD64-RHEL5.opengl.tar.gz

my build has the following options

    LINUXAMD64 SURF STRIDE OPENGL TACHYON IMD NOSILENT TCL TK FLTK
    PYTHON PTHREADS

Burlen

On 4/1/2015 7:51 AM, John Stone 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)