VMD-L Mailing List

From: Pawel Kedzierski (pawel.kedzierski_at_pwr.edu.pl)
Date: Wed Oct 11 2017 - 03:39:23 CDT

Many thanks John, it works fine with this workaround.
Pawel

W dniu 10.10.2017 o 17:10, John Stone pisze:
> 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