VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jan 25 2021 - 23:47:58 CST

Hi,
  I expect that the problem here is the specific graphics driver
on the machine you're using. The easiest things you could try
would be to look at upgrading the video driver, disabling the
"Composite" X-windows extension which has caused problems in
combination with some video drivers, and lastly overriding the
graphics driver and forcing the use of software-based OpenGL
rendering. I'm surprised that this hardware only has 2 CPU cores,
what kind of machine is it?

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jan 12, 2021 at 02:51:24PM +0000, Arham Amouei wrote:
> Dear John Stone,
>
> Many thanks for your time and the reply. Here are the messages VMD shows:
>
> /usr/local/lib/vmd/vmd_LINUXAMD64: /lib/x86_64-linux-gnu/libGL.so.1: no version information available (required by /usr/local/lib/vmd/vmd_LINUXAMD64)
> Info) VMD for LINUXAMD64, version 1.9.3 (November 30, 2016)
> 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, 2 CPUs detected.
> Info) CPU features: SSE2
> Info) Free system memory: 3242MB (83%)
> Info) No CUDA accelerator devices available.
> Warning) Detected X11 'Composite' extension: if incorrect display occurs
> Warning) try disabling this X server option. Most OpenGL drivers
> Warning) disable stereoscopic display when 'Composite' is enabled.
> Info) OpenGL renderer: Mesa DRI Mobile Intel® GM45 Express Chipset (CTG)
> Info) Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVF)
> Info) Full GLSL rendering mode is available.
> Info) Textures: 2-D (8192x8192), 3-D (512x512x512), Multitexture (8)
> Info) Dynamically loaded 2 plugins in directory:
> Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
>
> By the way, I don't face this problem with VMD 1.9.3 on Windows on another machine.
>
> Kind regards,
> Arham Amouei
>
> ????????????????????? Original Message ?????????????????????
> On Tuesday, January 12, 2021 1:59 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> > Hi,
> > It sounds to me like you're experiencing an issue with the behavior
> > of the graphics drivers on Ubuntu. What do the VMD startup messages
> > say in the text console when it first starts? I'm particularly interested
> > in the messages associated with the OpenGL renderer. If you have a buggy
> > OpenGL driver, then you may want/need to use one of the other rendering
> > approaches such as TachyonInternal instead of snapshot.
> >
> > Best,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Sun, Jan 10, 2021 at 10:17:35AM +0000, Arham Amouie wrote:
> >
> > > Hello
> > > I use VMD 1.9.3 on Kubuntu 20.04 on a rather old laptop. I'm trying to
> > > make a simple animation from hundreds of xyz files produced with a
> > > simulation. Here is the script for rendering the frames:
> > > display resize 389 343
> > > display nearclip set 0.001
> > > set indir "in/"
> > > set outdir "images/"
> > > for {set filenum 0} {$filenum <= 692} {incr filenum 1} {
> > > mol new [format "%s%05d.xyz" $indir $filenum] type {xyz} first 0 last
> > > -1 step 1 waitfor -1
> > > molinfo top set {center_matrix rotate_matrix scale_matrix
> > > global_matrix} {{{1 0 0 -885.859} {0 1 0 -750.065} {0 0 1 -750.047} {0 0 0
> > > 1}} {{1 0 0 0} {0 1 0 0} {0 0 1 0} {0 0 0 1}} {{0.00180681 0 0 0} {0
> > > 0.00180681 0 0} {0 0 0.00180681 0} {0 0 0 1}} {{1 0 0 0.78} {0 1 0 0.05}
> > > {0 0 1 0} {0 0 0 1}}}
> > > rotate x by $filenum
> > >
> > > mol modstyle 0 top Points 1.000000
> > > render snapshot [format "%s%05d.tga" $outdir $filenum]
> > > mol delete top
> > >
> > >
> > > }
> > > Each xyz file contains ~1.5 million atoms and I'm sure that the xyz files
> > > are not corrupted.
> > > Now, the problem is that some of the rendered images are irrelevent/wrong.
> > > For example, some of the saved frames show a black screen with VMD logo on
> > > it. I also used 'display update' and 'sleep 2' before the render command,
> > > but they didn't help.
> > > Kind regards,
> > > Arham Amouei
> >
> > --
> >
> > NIH Center 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/
>
> 

-- 
NIH Center 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/