VMD-L Mailing List

From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Mon Nov 28 2011 - 02:54:17 CST

On Friday 25 November 2011 16:38:01 Axel Kohlmeyer wrote:
> bjoern,
>
> it looks like you have saved the state after
> having worked with a huge number of molecules.
>
Indeed.
To be exact 50000 PDB files.

> it is quite possible, that you have triggered some
> internal and hard to track down VMD bug.
>
I am glad I could help ;-)

> i see two things that you can do:
> a) launch VMD with -debug and then trigger
> the "hang" again and then do a kill -STOP
> to the "stuck" VMD process and try to get
> a stack trace so that we get an idea what
> is going on.
>
Program received signal SIGSTOP, Stopped (signal).
0x00007ffff633f0ae in Tcl_ParseBraces () from /usr/lib64/libtcl8.5.so
(gdb)
(gdb) backtrace
#0 0x00007ffff633f0ae in Tcl_ParseBraces () from /usr/lib64/libtcl8.5.so
#1 0x00007ffff633f822 in Tcl_ParseCommand () from /usr/lib64/libtcl8.5.so
#2 0x00007ffff6340086 in ?? () from /usr/lib64/libtcl8.5.so
#3 0x000000000059207d in TclTextInterp::evalFile(char const*) ()
#4 0x0000000000592991 in ?? ()
#5 0x00007ffff62c97b6 in TclInvokeStringCommand () from
/usr/lib64/libtcl8.5.so
#6 0x00007ffff62cd686 in ?? () from /usr/lib64/libtcl8.5.so
#7 0x00007ffff630d6f9 in ?? () from /usr/lib64/libtcl8.5.so
#8 0x00007ffff6314785 in ?? () from /usr/lib64/libtcl8.5.so
#9 0x00007ffff62cf44d in TclEvalObjEx () from /usr/lib64/libtcl8.5.so
#10 0x00007ffff631a2ec in Tcl_RecordAndEvalObj () from /usr/lib64/libtcl8.5.so
#11 0x00007ffff631a356 in Tcl_RecordAndEval () from /usr/lib64/libtcl8.5.so
#12 0x000000000059236d in TclTextInterp::evalString(char const*) ()
#13 0x00000000005521d1 in UIText::act_on_command(int, Command*) ()
#14 0x000000000049ec3a in CommandQueue::runcommand(Command*) ()
#15 0x00000000005c7974 in ?? ()
#16 0x00007ffff5fe5171 in Fl_Menu_::picked(Fl_Menu_Item const*) () from
/usr/lib64/fltk-1/libfltk.so.1.3
#17 0x00007ffff5fe58fc in Fl_Menu_Bar::handle(int) () from
/usr/lib64/fltk-1/libfltk.so.1.3
#18 0x00007ffff5fd3d7c in Fl_Group::handle(int) () from
/usr/lib64/fltk-1/libfltk.so.1.3
#19 0x00007ffff5fc1066 in ?? () from /usr/lib64/fltk-1/libfltk.so.1.3
#20 0x00007ffff5fc1bed in Fl::handle_(int, Fl_Window*) () from
/usr/lib64/fltk-1/libfltk.so.1.3
#21 0x00007ffff600d8de in fl_handle(_XEvent const&) () from
/usr/lib64/fltk-1/libfltk.so.1.3
#22 0x00007ffff600ef54 in ?? () from /usr/lib64/fltk-1/libfltk.so.1.3
#23 0x00007ffff600f3a0 in fl_wait(double) () from
/usr/lib64/fltk-1/libfltk.so.1.3
#24 0x00007ffff5fc2954 in Fl::wait(double) () from
/usr/lib64/fltk-1/libfltk.so.1.3
#25 0x0000000000578c09 in main ()
(gdb)

Sending CONT and stopping it after some times yields the following:

(gdb)
Continuing.

Program received signal SIGSTOP, Stopped (signal).
[Switching to Thread 0x7ffff0165700 (LWP 840)]
0x00007ffff5340a93 in select () from /lib64/libc.so.6
(gdb) backtrace
#0 0x00007ffff5340a93 in select () from /lib64/libc.so.6
#1 0x00007ffff1281ddb in ?? () from /usr/lib64/libcuda.so
#2 0x00007ffff0d896bb in ?? () from /usr/lib64/libcuda.so
#3 0x00007ffff1282cb9 in ?? () from /usr/lib64/libcuda.so
#4 0x00007ffff6c35b5b in start_thread () from /lib64/libpthread.so.0
#5 0x00007ffff53469dd in clone () from /lib64/libc.so.6
(gdb)

and one more:

Program received signal SIGCONT, Continued.
[Switching to Thread 0x7ffff0a66700 (LWP 839)]
0x00007ffff6c39f3c in pthread_cond_wait@@GLIBC_2.3.2 () from
/lib64/libpthread.so.0
(gdb)
Continuing.

Program received signal SIGSTOP, Stopped (signal).
[Switching to Thread 0x7ffff7faf740 (LWP 835)]
0x00007ffff633f0bb in Tcl_ParseBraces () from /usr/lib64/libtcl8.5.so
(gdb) backtrace
#0 0x00007ffff633f0bb in Tcl_ParseBraces () from /usr/lib64/libtcl8.5.so
#1 0x00007ffff633f822 in Tcl_ParseCommand () from /usr/lib64/libtcl8.5.so
#2 0x00007ffff6340086 in ?? () from /usr/lib64/libtcl8.5.so
#3 0x000000000059207d in TclTextInterp::evalFile(char const*) ()
#4 0x0000000000592991 in ?? ()
#5 0x00007ffff62c97b6 in TclInvokeStringCommand () from
/usr/lib64/libtcl8.5.so
#6 0x00007ffff62cd686 in ?? () from /usr/lib64/libtcl8.5.so
#7 0x00007ffff630d6f9 in ?? () from /usr/lib64/libtcl8.5.so
#8 0x00007ffff6314785 in ?? () from /usr/lib64/libtcl8.5.so
#9 0x00007ffff62cf44d in TclEvalObjEx () from /usr/lib64/libtcl8.5.so
#10 0x00007ffff631a2ec in Tcl_RecordAndEvalObj () from /usr/lib64/libtcl8.5.so
#11 0x00007ffff631a356 in Tcl_RecordAndEval () from /usr/lib64/libtcl8.5.so
#12 0x000000000059236d in TclTextInterp::evalString(char const*) ()
#13 0x00000000005521d1 in UIText::act_on_command(int, Command*) ()
#14 0x000000000049ec3a in CommandQueue::runcommand(Command*) ()
#15 0x00000000005c7974 in ?? ()
#16 0x00007ffff5fe5171 in Fl_Menu_::picked(Fl_Menu_Item const*) () from
/usr/lib64/fltk-1/libfltk.so.1.3
#17 0x00007ffff5fe58fc in Fl_Menu_Bar::handle(int) () from
/usr/lib64/fltk-1/libfltk.so.1.3
#18 0x00007ffff5fd3d7c in Fl_Group::handle(int) () from
/usr/lib64/fltk-1/libfltk.so.1.3
#19 0x00007ffff5fc1066 in ?? () from /usr/lib64/fltk-1/libfltk.so.1.3
#20 0x00007ffff5fc1bed in Fl::handle_(int, Fl_Window*) () from
/usr/lib64/fltk-1/libfltk.so.1.3
#21 0x00007ffff600d8de in fl_handle(_XEvent const&) () from
/usr/lib64/fltk-1/libfltk.so.1.3
#22 0x00007ffff600ef54 in ?? () from /usr/lib64/fltk-1/libfltk.so.1.3
#23 0x00007ffff600f3a0 in fl_wait(double) () from
/usr/lib64/fltk-1/libfltk.so.1.3
#24 0x00007ffff5fc2954 in Fl::wait(double) () from
/usr/lib64/fltk-1/libfltk.so.1.3
#25 0x0000000000578c09 in main ()
(gdb)

> b) use a text editor to trim off all the useless
> script code. a saved state usually is very verbose
> but for the most part, the script code produced
> is identical with the default, so it would not really
> be needed. that is particularly true for the color
> table settings. with such a lean and mean state,
> you may not run into any problems.
>
Removing the color definitions as suggested by Ajasja Ljubetič helped...

Anything more I can do to help?

> cheers,
> axel.
>
Thanks,
Bjoern

> On Fri, Nov 25, 2011 at 1:51 AM, Bjoern Olausson
>
> <namdlist_at_googlemail.com> wrote:
> > Hi,
> >
> > I generated some representations via a script and saved the view with
> > "save_state" command.
> >
> > When i load this state file, VMD reads it, does everything what I expect
> > it to do, shows the final representation as expected, but then VMD is
> > unresponsive has 100% CPU usage and all VMD related window, except the
> > cmd, are neither updated nor usable. I have to kill the VMD process..
> >
> > I am running VMD 1.9 on Linux 3.0.6 with 8GB RAM, a GeForce 8600 GT and a
> > Core2 Quad CPU Q9300 - composing is disabled for KDE.
> >
> > You can find the state file here:
> > http://paste.pocoo.org/show/512658/
> >
> > An here's the output of VMD when reading this file (vmd -e statfile.vmd):
> > http://paste.pocoo.org/show/512659/
> >
> > Any ideas?
> >
> > Cheers,
> > Bjoern
> >
> > --
> > Bjoern Olausson
> > Martin-Luther-Universität Halle-Wittenberg
> > Institut für Pharmazie
> > Wolfgang-Langenbeck-Str.4
> > 06120 Halle/Saale
> >
> > Phone: +49-345-55-25122 

-- 
Bjoern Olausson
Martin-Luther-Universität Halle-Wittenberg 
Institut für Pharmazie
Wolfgang-Langenbeck-Str.4
06120 Halle/Saale
Phone: +49-345-55-25122