VMD-L Mailing List

From: Peter C. Lai (pcl_at_uab.edu)
Date: Tue May 29 2012 - 12:51:51 CDT

Did you try a combination of turning off compositing on either side? That
extension could be wacky with remote X going on. The other possibility is
your link is too slow between the host and client (not to mention the X
protocol is inefficient to begin with; and if you are tunneling this over
SSH god help you).

Also what representatoin is this happening with (Lines etc.)?

In addition, locally you are using VMD 1.9 and not 1.9.1 as demonstrated in
the version strings. (not like this matters operationally, but you're still
not comparing 1.9.1 locally).

Finally, take a look at the 2 opengl feature strings:
Local 1.9
> Info) Features: STENCIL MSAA(16) MDE CVA MTX NPOT PP PS GLSL(OVF)
Remote 1.9.1
> Info) Features: STENCIL MSAA(8) MDE MTX NPOT PP PS

This could have something to do with it too, dunno.

On 2012-05-29 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 

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