VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Apr 01 2015 - 13:34:18 CDT

Hi,
  I still wonder about this, as the ulimit values you've reported
don't seem wildly out of whack compared to mine:
  bash-3.00$ ulimit -s -v
  stack size (kbytes, -s) 10240
  virtual memory (kbytes, -v) unlimited

That said, there may very well be some strange behavior in your
pthreads implementation that relates to the stack size, and if
limiting your VMD process to 4 threads cures the problem, that
seems reasonable if your sysadmins aren't willing to adjust the
process limits otherwise.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Apr 01, 2015 at 11:22:20AM -0700, Burlen Loring wrote:
> It works up to 4 threads! the ulimits are
>
> stack size (kbytes, -s) 262144
> virtual memory (kbytes, -v) 2097152
>
> vm is restricted on the login node to 2GB. It's not allowed for us to
> change these ulimits... I think 4 threads is good enough! We can consider
> the issue solved if you like.
>
> Thanks for your help!
> Burlen
>
> On 4/1/2015 11:01 AM, Axel Kohlmeyer wrote:
>
> hmm... what is the stack size limit on those machines?
> for multi-threaded operations, especially with many CPU cores
> available, you may run out of stack space.
>
> also, you could try limiting the number of available threads to 1
> using the environment variable VMDFORCECPUCOUNT
>
> axel.
>
> On Wed, Apr 1, 2015 at 1:09 PM, Burlen Loring [1]<burlen.loring_at_gmail.com> wrote:
>
> 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) [2]http://www.ks.uiuc.edu/Research/vmd/
> Info) Email questions and bug reports to [3]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
> [4]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
> [5]<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:
> [6]<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) [7]http://www.ks.uiuc.edu/Research/vmd/
> Info) Email questions and bug reports to [8]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)
>
> References
>
> Visible links
> 1. mailto:burlen.loring_at_gmail.com
> 2. http://www.ks.uiuc.edu/Research/vmd/
> 3. mailto:vmd_at_ks.uiuc.edu
> 4. mailto:vmd_at_ks.uiuc.edu
> 5. http://gnu.org/licenses/gpl.html
> 6. http://www.gnu.org/software/gdb/bugs/
> 7. http://www.ks.uiuc.edu/Research/vmd/
> 8. mailto:vmd_at_ks.uiuc.edu 

-- 
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/