VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Oct 10 2017 - 10:10:58 CDT

Pawel,
  There is an issue with the version of OptiX I compiled
the currently-posted VMD 1.9.4 alpha against, it can segfault during
startup on machines that have no NVIDIA driver software.
You can get past this by setting the environment variable VMDNOOPTIX before
you run VMD, e.g.:
  /bin/bash:
     export VMDNOOPTIX=1
  /bin/csh:
     setenv VMDNOOPTIX 1

I expect the next VMD test builds I post will be compiled against a
test version of OptiX that contains a fix for that problem so the
environment variables should no longer be necessary.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Oct 10, 2017 at 01:21:30PM +0200, Pawel Kedzierski wrote:
> W dniu 10.10.2017 o 10:45, Pawel Kedzierski pisze:
>
> Dear all,
>
> Apparently, VMD 1.9.4 alpha 8 crashes locally too, when using Intel DRI
> linux drivers. Checked on Ubuntu 16.04 laptop (OpenGL renderer: Mesa DRI
> Intel(R) Sandybridge Mobile) and on Debian Jessie desktop (Mesa DRI
> Intel(R) Haswell Desktop).
> On the same laptop and os but using Nvidia drivers through optirun, it
> starts just fine (OpenGL renderer: GeForce GT 540M/PCIe/SSE2)
> Is it a feature, that non-nvidia/low-end/software rendered graphics is not
> supported at all?
> Thanks,
> Pawel
>
> /usr/local/vmd1.9.4a8/vmd_LINUXAMD64:
> /usr/lib/x86_64-linux-gnu/libGL.so.1: no version information available
> (required by /usr/local/vmd1.9.4a8/vmd_LINUXAMD64)
> Info) VMD for LINUXAMD64, version 1.9.4a8 (August 30, 2017)
> Info) [1]http://www.ks.uiuc.edu/Research/vmd/
> Info) Email questions and bug reports to [2]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) CPU features: SSE2 AVX AVX2 FMA
> Info) Free system memory: 7394MB (93%)
> 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 Intel(R) Haswell Desktop
> Info) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVFS)
> Info) Full GLSL rendering mode is available.
> Info) Textures: 2-D (8192x8192), 3-D (512x512x512), Multitexture (8)
> Segmentation fault
>
> I have just tried the alpha version of VMD (1.9.4 alpha 8) and I
> discovered that it crashes when run remotely. I guess the problem is
> that the X11 connection (forwarded via ssh) switches the OpenGL renderer
> to the software one. It is always the case, independently on the method
> of connection - I tried "ssh -X" and X2Go Client from Ubuntu 16.04, and
> also MobaXterm from Windows 10. The result is always this:
>
> /usr/local/vmd1.9.4a8/vmd_LINUXAMD64:
> /usr/lib/x86_64-linux-gnu/libGL.so.1: no version information available
> (required by /usr/local/vmd1.9.4a8/vmd_LINUXAMD64)
> Info) VMD for LINUXAMD64, version 1.9.4a8 (August 30, 2017)
> Info) [3]http://www.ks.uiuc.edu/Research/vmd/
> Info) Email questions and bug reports to [4]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) CPU features: SSE2 AVX AVX2 FMA
> Info) Free system memory: 7448MB (94%)
> 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: Gallium 0.4 on llvmpipe (LLVM 3.5, 256 bits)
> 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)
> Segmentation fault
>
> I know that the Gallium renderer crashes Pymol too, but VMD 1.9.2 used
> to work (I haven't tried 1.9.3). So my questions are:
>
> - it is expected not to work for this renderer? and if yes,
>
> - does someone know a solution to make the forwarded X11 session use a
> working OpenGL renderer?
>
> Thanks in advance,
>
> Pawel
>
> References
>
> Visible links
> 1. http://www.ks.uiuc.edu/Research/vmd/
> 2. mailto:vmd_at_ks.uiuc.edu
> 3. http://www.ks.uiuc.edu/Research/vmd/
> 4. mailto:vmd_at_ks.uiuc.edu

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> org;quoted-printable:Wroc=C5=82aw University of Technology, Faculty of Chemistry;Advanced Materials Engineering and Modelling Group
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> email;internet:Pawel.Kedzierski_at_pwr.edu.pl
> tel;work:+48 71 3203200
> tel;fax:+48 71 3203364
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> 

-- 
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/