VMD-L Mailing List

From: lucie delemotte (lucie.delemotte_at_edam.uhp-nancy.fr)
Date: Fri Jun 12 2009 - 11:17:35 CDT

Hi!
Working here too!
Thanks a lot!
Lucie

On Fri, Jun 12, 2009 at 4:44 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> Marius,
> Great, I'll add this to the Linux release notes in case other people
> encounter the problem before NVIDIA has a chance to release updated drivers
> that fix the problem.
>
> Cheers,
> John Stone
> johns_at_ks.uiuc.edu
>
> On Fri, Jun 12, 2009 at 03:47:39PM +0200, Marius Retegan wrote:
> > Works now. Thanks
> > Marius
> >
> > On Fri, Jun 12, 2009 at 4:30 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> > >
> > > Marius, Lucie,
> > > NVIDIA engineers were able to reproduce the hanging problem today
> > > and they provided us with a suggestion for a workaround which worked
> > > when Axel and I tried it on one of this machines here at U. Penn
> > > (I'm visiting Axel this week).
> > >
> > > Try adding this extra config line to the device section
> > > of your /etc/X11/xorg.conf config file:
> > > Option "ConstantFrameRateHint" "True"
> > >
> > > This apparently disables some performance optimizations, but
> > > results in stable behavior in the case of the problem you're
> > > experiencing with the most recent linux distros and the new
> > > NVIDIA drivers. Let us know if this solves the problem for you
> > > on your machines. This is what the NVIDIA engineers suggested
> > > we try, and it worked for Axel and I on his test box.
> > >
> > > NVIDIA has a bug filed on this and whenever a production driver is
> > > available that fixes the problem, I'll post a note to VMD-L.
> > > For now, I suggest adding the config line above and use it as
> > > a short-term remedy, so that you can still use CUDA and other
> > > advanced features of the latest NVIDIA drivers.
> > >
> > > Cheers,
> > > John Stone
> > > vmd_at_ks.uiuc.edu
> > >
> > > On Thu, Jun 11, 2009 at 08:59:54AM -0500, John Stone wrote:
> > > >
> > > > Marius, Lucie,
> > > > Axel and I did some testing (I'm at U. Penn. visiting his lab this
> > > week)
> > > > and it seems that the Fedora "legacy" NVIDIA 173.xx driver package
> > > > works fine also. I am in contact with the driver team at NVIDIA and
> > > > they are working on reproducing the problem in their lab currently.
> > > > If they can reproduce the problem in their lab, then they should be
> > > > able to tell us more about what's going on here. In the short term,
> > > > using the 173.xx driver series looks like it may be a viable
> workaround
> > > > until we have a better solution.
> > > >
> > > > Cheers,
> > > > John Stone
> > > > vmd_at_ks.uiuc.edu
> > > >
> > > > On Thu, Jun 11, 2009 at 09:43:05AM +0200, Marius Retegan wrote:
> > > > > Yesterday I also did a simple test. While rebooting with an older
> > > kernel for
> > > > > which
> > > > > I have only the nouveau drivers I didn't noticed any problems
> while
> > > running
> > > > > VMD.
> > > > > So as you said it's possible that this whole thing is not related
> to
> > > VMD.
> > > > > Anyway thank you.
> > > > > Marius
> > > > >
> > > > > On Wed, Jun 10, 2009 at 6:47 PM, John Stone <johns_at_ks.uiuc.edu>
> wrote:
> > > > >
> > > > > >
> > > > > > 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/>
> > > <http://www.ks.uiuc.edu/%7Ejohns/><
> > > > > > 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/>
> <http://www.ks.uiuc.edu/%7Ejohns/><
> > > 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/><
> 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/><
> 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/ <http://www.ks.uiuc.edu/%7Ejohns/>
> Fax: 217-244-6078
>