VMD-L Mailing List

From: Burlen Loring (burlen.loring_at_gmail.com)
Date: Wed Apr 01 2015 - 13:22:20 CDT

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 <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) 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)
>>
>>
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