VMD-L Mailing List

From: Dallas Warren (dallas.warren_at_monash.edu)
Date: Mon Apr 29 2019 - 18:59:40 CDT

Actually, I got those speeds wrong, apologies for that.

a8 with RTX 2080Ti 20.33 sec
a31 with RTX 1080Ti 3.33 sec.

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, 30 Apr 2019 at 09:52, Dallas Warren <dallas.warren_at_monash.edu> wrote:
>
> 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/
> >