VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Nov 30 2011 - 09:50:16 CST
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Bjoern,
I'll have a look at this in the next few days. It sounds to me
like the VMD save_state script needs to be revised to handle the
50,000 molecule case more gracefully. From your description,
it sounds that it's emitting color state info for every molecule ID
that ever existed, and not just the ones that are currently active.
I'll have a look at this and let you know what I find.
Cheers,
John Stone
vmd_at_ks.uiuc.edu
On Mon, Nov 28, 2011 at 09:54:17AM +0100, Bjoern Olausson wrote:
> 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 Ljubeti?? 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
-- NIH Resource 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/ Fax: 217-244-6078
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