VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Apr 29 2019 - 21:09:42 CDT

Dallas,
  If you happen to have the exact input files that relate to the
message you got below, I would love to get a copy of them to use
in exercising the code while under a cudamemcheck run. It is possible
that what you observed is some weird transient GPU driver oops,
but is also possible you've found a rare bug, and if so I'd
like to try and catch it.

Best,
  John

On Tue, Apr 30, 2019 at 09:52:15AM +1000, Dallas Warren wrote:
> John,

[...]

> 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/
> > 

-- 
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/