VMD-L Mailing List

From: Dallas Warren (dallas.warren_at_monash.edu)
Date: Mon Apr 29 2019 - 18:52:15 CDT

John,

In terms of rendering speed with TachyonL-OptiX, a8 with GTX 1080Ti a
scene took 20.33 sec, a31 with RTX 1080Ti same scene was 3.33 sec.

This is mainly for future possible use and your information, as it
failed, then I restarted it and then it worked. So nothing to do
right now, I will email again if the problem persists at a later date.

I have just installed my RTX 2080Ti, updated the nvidia drivers,
installed 1.9.4a31 and attempted to render a scene using
TachyonL-OptiX(internal) of a QuickSurf with the Blownglass material.
It works using a8 and fails with a31.

Here is the terminal output, a8 first, followed by a31:

dallas_at_morph:~/Pictures/vmd> vmd_1.9.4a8
/usr/local/lib/vmd_1.9.4a8/vmd_LINUXAMD64: /usr/lib64/libGL.so.1: no
version information available (required by
/usr/local/lib/vmd_1.9.4a8/vmd_LINUXAMD64)
Info) VMD for LINUXAMD64, version 1.9.4a8 (August 30, 2017)
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, 12 CPUs detected.
Info) CPU features: SSE2 AVX
Info) Free system memory: 34GB (96%)
Info) Creating CUDA device pool and initializing hardware...
Info) Detected 1 available CUDA accelerator:
Info) [0] GeForce RTX 2080 Ti 68 SM_7.5 @ 1.63 GHz, 11GB RAM, KTO, AE3, ZCP
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: GeForce RTX 2080 Ti/PCIe/SSE2
Info) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVFGS)
Info) Full GLSL rendering mode is available.
Info) Textures: 2-D (32768x32768), 3-D (16384x16384x16384), Multitexture (4)
Info) Detected 1 available TachyonL/OptiX ray tracing accelerator
Info) Compiling 1 OptiX shaders on 1 target GPU...
Info) Dynamically loaded 2 plugins in directory:
Info) /usr/local/lib/vmd_1.9.4a8/plugins/LINUXAMD64/molfile
after#0
vmd > Info) Using plugin gro for structure file
/home/dallas/experiments/current/19-034/run_files/md_0.gro
Info) Using plugin gro for coordinates from file
/home/dallas/experiments/current/19-034/run_files/md_0.gro
Info) Determining bond structure from distance search ...
Info) Analyzing structure ...
Info) Atoms: 49203
Info) Bonds: 44706
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 4497
Info) Waters: 3345
Info) Segments: 1
Info) Fragments: 4497 Protein: 0 Nucleic: 0
Info) Finished with coordinate file
/home/dallas/experiments/current/19-034/run_files/md_0.gro.
Info) Rendering current scene to 'vmdscene.ppm' ...
Info) Ambient occlusion enabled.
Info) Shadow rendering enabled.
OptiXDisplayDevice) Total rendering time: 20.23 sec
Info) Executing post-render cmd 'display vmdscene.ppm' ...
Info) Rendering complete.
Info) VMD for LINUXAMD64, version 1.9.4a8 (August 30, 2017)
Info) Exiting normally.

dallas_at_morph:~/Pictures/vmd> vmd_1.9.4a31
/usr/local/lib/vmd_1.9.4a31/vmd_LINUXAMD64: /usr/lib64/libGL.so.1: no
version information available (required by
/usr/local/lib/vmd_1.9.4a31/vmd_LINUXAMD64)
Info) VMD for LINUXAMD64, version 1.9.4a31 (March 13, 2019)
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, 12 CPUs detected.
Info) CPU features: SSE2 AVX
Info) Free system memory: 34GB (95%)
Info) Creating CUDA device pool and initializing hardware...
Info) Detected 1 available CUDA accelerator:
Info) [0] GeForce RTX 2080 Ti 68 SM_7.5 1.63 GHz, 11GB RAM, KTO, AE3, ZCP
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: GeForce RTX 2080 Ti/PCIe/SSE2
Info) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVFGS)
Info) Full GLSL rendering mode is available.
Info) Textures: 2-D (32768x32768), 3-D (16384x16384x16384), Multitexture (4)
Info) Detected 1 available TachyonL/OptiX ray tracing accelerator
Info) Compiling 1 OptiX shaders on 1 target GPU...
Info) Dynamically loaded 3 plugins in directory:
Info) /usr/local/lib/vmd_1.9.4a31/plugins/LINUXAMD64/molfile
after#0
vmd > Info) Using plugin gro for structure file
/home/dallas/experiments/current/19-034/run_files/md_0.gro
Info) Using plugin gro for coordinates from file
/home/dallas/experiments/current/19-034/run_files/md_0.gro
Info) Determining bond structure from distance search ...
Info) Analyzing structure ...
Info) Atoms: 49203
Info) Bonds: 44706
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 4497
Info) Waters: 3345
Info) Segments: 1
Info) Fragments: 4497 Protein: 0 Nucleic: 0
Info) Finished with coordinate file
/home/dallas/experiments/current/19-034/run_files/md_0.gro.
CUDA error: an illegal memory access was encountered, CUDAQuickSurf.cu line 1402
CUDA Thrust sort_by_key() failed: CUDASort.cu line 190
dev_radix_sort_by_key() failed: CUDASpatialSearch.cu line 259
Info) Rendering current scene to 'vmdscene.ppm' ...
Info) Ambient occlusion enabled.
Info) Shadow rendering enabled.
Segmentation fault (core dumped)

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren_at_monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.

On Tue, 26 Feb 2019 at 14:40, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> Now that the NVIDIA drivers with RTX support are generally
> available, I have made a current 64-bit Linux test build of VMD 1.9.4 (a29)
> that includes RTX hardware-accelerated ray tracing, and it is
> posted on the web site. To use this version you will need the latest
> NVIDIA 418.xx (where xx >= 30) driver version from the NVIDIA web site.
>
> VMD users should expect TachyonLOPtiX ray tracing performance gains
> that range as high as 8x faster when comparing the new RTX GPUs with
> the new VMD with prior versions of VMD running on so-called
> Pascal and Volta class NVIDIA GPUs.
>
> Best regards,
> John Stone
> vmd_at_ks.uiuc.edu
>
> --
> 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/
>