VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Dec 08 2009 - 16:53:15 CST

On Tue, 2009-12-08 at 12:34 -0600, John Stone wrote:
> Hi Rob,
> Appearances can be deceiving. I've got a lot of experience debugging
> broken graphics drivers, and I can tell you that the odds currently lay
> heavily in favor of your video driver being broken. The most complex parts
> of the VMD graphics code are not engaged until one actually loads a
> molecule and starts rendering. From the log you provided in your previous
> email, it looks to me like you're not even getting completely through
> startup before you're getting a crash, which is a strong indicator of
> buggy drivers. The only things that VMD is doing at that early point
> in the startup are:
> 1) creating X11 window and associated OpenGL context
> 2) compiling GLSL shaders and enabling them if possible
>
> My feeling is that you're crashing due to bugs in your driver's
> implementation of GLSL, because that's the only code that changed
> much from VMD 1.8.6 to VMD 1.8.7. The GLSL code isn't even compiled
> into VMD in fact, it is loaded by VMD and compiled by the OpenGL driver
> at runtime, and if I were to guess, this is probably where your problem
> is occuring.

to add one important(?) detail to the discussion. as of fedora 12,
the default driver for nvidia hardware is the nouveau driver
instead of the older nv driver. both drivers are sub-standard
compared to the nvidia drivers (which can be installed and easily
maintained through incorporating the rpmfusion repository. i've
been doing this very successfully for years with its predecessor
rpm.livna.org), but especially the nouveau driver claims to have
3d support which is pretty much work in progress, but like the
intel graphics drivers in xorg they all leave a lot to be desired
if you care about anything in OpenGL besides the composite extension
and running glxgears.

the prickly issue is whether fedora 12 is already fully supported
by the latest nvidia driver. with fedora, ubuntu and other linux
distribution push developments similarly aggressively forward,
it is always a good idea to let a couple of months pass until
before installing it on any hardware that is used for production.

cheers,
    axel.

> Rather than guess however, you can do a couple of simple tests and
> see how far VMD got when the crash occured, by running it like this:
> vmd -debug
>
> Once it crashes, type the command "where" into your gdb session, and
> that should display a stack trace that shows where the crash is occuring.
> We know from your previous log that the crash is occuring inside of one
> of the X11 libraries, but we don't know at what point in the VMD code this
> was occuring, so running the debugger and getting the traceback with
> "where" should also tell us what routine we were in within the VMD code
> when the crash occurs, which should tell me what I need to know to track
> down the cause of your problem.
>
> I still think you have a 95% chance of a bad video driver as I said before,
> but I'm happy to help narrow this down so you can get past this problem.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Dec 08, 2009 at 06:05:26AM -0800, Rob wrote:
> >
> > John Stone wrote on Mon Dec 07 2009:
> > >
> > > You need to install the proper NVIDIA drivers for your
> > > machine. The OpenGL that's currently active is a software
> > > rasterizer, and that's definitely _not_ what you want to be using...
> >
> > I have two PCs with same Nvidia cards "GeForce 8600 GTS (rev a1)".
> > One PC is 32 bits with Fedora 12 and here VMD 1.8.7 runs just fine.
> > The other PC is 64 bits with Fedora 12 and here VMD 1.8.7 segfaults.
> >
> > On the 64 bits system, VMD version 1.8.6 runs fine.....
> >
> > See below for more details.
> >
> > Does all this make sense?
> > So to me it appears that it's not, as you say, that the Fedora NVidia
> > drivers are always bad.....
> >
> > Could it be that there's a bug in 1.8.7 that causes the segfault?
> > Or will you tell me that specifically the 64 bits system needs the
> > proper NVIDIA drivers?
> >
> > Thanks.
> > Rob.
> >
> >
> > Here is what I get with VMD 1.8.7 32bits Fedora 12:
> >
> > $ vmd
> > Info) VMD for LINUX, version 1.8.7 (August 1, 2009)
> > 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, 4 CPUs detected.
> > Info) Free system memory: 1337MB (66%)
> > Info) No CUDA accelerator devices available.
> > Warning) Detected X11 'Composite' extension: if incorrect display occurs
> > Warning) try disabling this optional X server feature.
> > Info) OpenGL renderer: Software Rasterizer
> > Info) Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVF)
> > Info) Full GLSL rendering mode is available.
> > Info) Textures: 2-D (4096x4096), 3-D (256x256x256), Multitexture (8)
> > vmd >
> >
> > Here is what I get with VMD 1.8.6 on 64bits Fedora 12:
> >
> > 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: 5237MB (87%)
> > Info) OpenGL renderer: Software Rasterizer
> > Info) Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVF)
> > Info) Full GLSL rendering mode is available.
> > Info) Textures: 2-D (4096x4096), 3-D (256x256x256), Multitexture (8)
> > vmd >
> >
> >
> > Here is what I get with VMD 1.8.7 on 64bits Fedora 12:
> >
> > Info) VMD for LINUXAMD64, version 1.8.7 (August 1, 2009)
> > 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: 5145MB (86%)
> > Info) No CUDA accelerator devices available.
> > Warning) Detected X11 'Composite' extension: if incorrect display occurs
> > Warning) try disabling this optional X server feature.
> > Info) OpenGL renderer: Software Rasterizer
> > Info) Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVF)
> > Info) Full GLSL rendering mode is available.
> > Info) Textures: 2-D (4096x4096), 3-D (256x256x256), Multitexture (8)
> > Segmentation fault
> >
> >
> >
> >
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com 
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.