VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jun 10 2009 - 11:47:28 CDT

Marius,
  Axel and I have been looking into this using a Fedora 11 machine
he just installed yesterday, and there's definitely something fishy
going on where the VMD process gets a signal, a signal handler runs
(apparrently in the OpenGL driver), and the OpenGL driver library
function calls malloc, and the whole process gets stuck in a glibc
malloc mutex call. My theory at present is that either
glibc has a malloc double locking bug, or the NVIDIA driver
should not be calling malloc in a signal handler. We won't know
more until we do some VMD compiles on Fedora 11 itself and see if
the same problem occurs when compiled against that libc/libstdc++ etc.

So far I see nothing to indicate that this is a problem in VMD itself.
We'll let you know what we find out after we do more testing.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jun 09, 2009 at 06:30:43PM +0200, Marius Retegan wrote:
> They release it today :)
> I've updated my system to the last stable repos and I've disabled rawhide
> repositories.
> Sure I can run the tests.
> Marius
>
> On Tue, Jun 9, 2009 at 6:26 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> >
> > Marius,
> > Which Fedora 11 beta release is this? They are expected to announce
> > the final version imminently, but last I checked they haven't released the
> > final version yet:
> > http://fedoraproject.org/wiki/Releases/11/Schedule
> >
> > If this is something specific to bleeding edge Fedora or other
> > distros, it may be a libc, libstc++, or Xlib binary compatibility
> > issue of some kind. If so, we could do builds specifically for
> > these platforms, but I'd prefer to find a solution that would allow
> > you to run the same binary that works everywhere else. If you're willing
> > to do some more testing for me, I might have a few ideas to try that
> > involve copying in various shared libraries to see if they have an effect.
> >
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Tue, Jun 09, 2009 at 06:07:25PM +0200, Marius Retegan wrote:
> > > Hi
> > >
> > > The OpenGL window always starts, but then VMD hangs. The main window (all
> > > the menus windows :) ) starts only if I go in debug mode.
> > > I've tried with and without Composit extension. Same result.
> > > Compiz is not enabled.
> > >
> > > On Tue, Jun 9, 2009 at 4:48 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
> > >
> > > >
> > > > Marius,
> > > > Interesting. Does the program hang, crash, or appears to start up
> > > > but you never see the OpenGL window? Do you have Compiz or the
> > Composite
> > > > extension enabled on this machine? (use xdpyinfo to query for this)
> > > >
> > > > Cheers,
> > > > John
> > > >
> > > > On Tue, Jun 09, 2009 at 09:08:37AM +0200, Marius Retegan wrote:
> > > > > I've tried the 185.18.14 driver. Strangely the main window doesn't
> > even
> > > > come
> > > > > up. VMD in debug mode works again.
> > > > > I can post any details about my system if necessary.
> > > > > Marius
> >
> > --
> > NIH Resource for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > WWW: http://www.ks.uiuc.edu/~johns/ <http://www.ks.uiuc.edu/%7Ejohns/>
> > Fax: 217-244-6078
> > 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078