VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue May 29 2012 - 11:01:26 CDT

Hi,
  This sounds like a display driver or X11 remote GLX issue of some kind.

Recently a number of Linux distributions have shipped versions of X windows
that have broken behavior for remote display. I've seen it occur with video
cards and drivers from multiple vendors, so the chances are high that it's
actually the X11 version you're using that's broken and not the video drivers,
but it is hard to say for sure. One thing that would help is to narrow down
the range of scenarios where you get the flickering.

Do you get flickering when you run other OpenGL programs like "glxgears",
or only when you run VMD? VMD is using a much broader range of OpenGL
features than simpler codes like the glxgears demo, but if you also see
flickering with such simple programs, then that would certainly demonstrate
that you've got some kind of problematic interaction between your X-windows
installations when doing remote display of OpenGL via remote GLX. I would
try running "glxgears" and then run a few other OpenGL programs and see
which ones experience the same problem. Working with more information
we may be able to come up with a solution or workaround for you.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, May 29, 2012 at 05:43:52PM +0200, Clarinet wrote:
>
> Dear,
>
> we have a strange variant of VMD/Radeon flickering display issue. We
> installed VMD 1.9.1 locally and on a remote server. When VMD runs
> locally, everything is OK and VMD works as it should. When VMD is run on
> a remote server with display set to the local machine (i.e. it runs on
> the server but opens windows on the local machine), the flickering
> problem appears - VMD windows draws improperly, sometimes it stays
> "empty" (only frame, transparent contents), sometimes it leaves its
> contents when the window is moved etc.
>
> The graphics card on the local computer is ATI radeon, OS is Ubuntu. I
> tried to play with VMDDISABLEATILINUXWORKAROUND and VMDDISABLESTEREO but
> it did not change anything.
>
> When started loaclly, VMD shows:
>
> Info) VMD for LINUXAMD64, version 1.9 (March 14, 2011)
> 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: 6640MB (82%)
> Info) No CUDA accelerator devices available.
> Warning) Detected X11 'Composite' extension: if incorrect display occurs
> Warning) try disabling this optional X server feature.
> Info) ATI Linux driver detected, limiting features to avoid driver bugs.
> Info) Set the environment variable VMDDISABLEATILINUXWORKAROUND
> Info) to enable full functionality on a known-safe driver version.
> Info) OpenGL renderer: ATI Radeon HD 3870
> Info) Features: STENCIL MSAA(16) MDE CVA MTX NPOT PP PS GLSL(OVF)
> Info) GLSL rendering mode is NOT available.
> Info) Textures: 2-D (8192x8192), 3-D (8192x8192x8192), Multitexture (8)
> Info) Dynamically loaded 2 plugins in directory:
> Info) /home/xxxxx/programs/vmd-1.9/plugins/LINUXAMD64/molfile
> Info) File loading in progress, please wait.
> Info) Using plugin pdb for structure file complex-13-o.pdb
> Info) Using plugin pdb for coordinates from file complex-13-o.pdb
> Info) Determining bond structure from distance search ...
> Info) Finished with coordinate file complex-13-o.pdb.
> Info) Analyzing structure ...
> Info) Atoms: 4614
> Info) Bonds: 4668
> Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
> Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
> Info) Residues: 288
> Info) Waters: 0
> Warning) Unusual bond between residues: 35 (protein) and 36 (none)
> Warning) Unusual bond between residues: 37 (none) and 38 (protein)
> Warning) Unusual bond between residues: 144 (protein) and 145 (none)
> Warning) Unusual bond between residues: 146 (none) and 147 (protein)
> Info) Segments: 1
> Info) Fragments: 8 Protein: 3 Nucleic: 0
>
> When started remotely, VMD displays:
>
> Info) VMD for LINUXAMD64, version 1.9.1 (February 1, 2012)
> 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: 11281MB (93%)
> Warning) Detected a mismatch between CUDA runtime and GPU driver
> Warning) Check to make sure that GPU drivers are up to date.
> 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: ATI Radeon HD 3870
> Info) Features: STENCIL MSAA(8) MDE MTX NPOT PP PS
> Info) GLSL rendering mode is NOT available.
> Info) Textures: 2-D (8192x8192), 3-D (8192x8192x8192), Multitexture (8)
> Info) Dynamically loaded 2 plugins in directory:
> Info)
> /usr/local/programs/common/vmd/vmd-1.9.1/arch/amd64/plugins/LINUXAMD64/molfile
> Info) File loading in progress, please wait.
> Info) Using plugin pdb for structure file final-cdk2.pdb
> Info) Using plugin pdb for coordinates from file final-cdk2.pdb
> Info) Determining bond structure from distance search ...
> Info) Finished with coordinate file final-cdk2.pdb.
> Info) Analyzing structure ...
> Info) Atoms: 4631
> Info) Bonds: 4690
> Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
> Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
> Info) Residues: 284
> Info) Waters: 0
> Warning) Unusual bond between residues: 35 (protein) and 36 (none)
> Warning) Unusual bond between residues: 37 (none) and 38 (protein)
> Warning) Unusual bond between residues: 144 (protein) and 145 (none)
> Warning) Unusual bond between residues: 146 (none) and 147 (protein)
> Info) Segments: 1
> Info) Fragments: 4 Protein: 3 Nucleic: 0
>
> Any ideas?
>
> Best regards,
>
> Jiri Polach 

-- 
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