From: Clarinet (clarinet_at_atlas.cz)
Date: Tue May 29 2012 - 10:43:52 CDT

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