VMD-L Mailing List

From: Nikhil Maroli (scinikhil_at_gmail.com)
Date: Fri Apr 16 2021 - 12:16:41 CDT

Thank you all, when I use VMD with optix +CUDA it works. Earlier I had only
CUDA.

On Thu, Apr 15, 2021 at 11:21 PM Jason Smith <jason_smith_18_at_sfu.ca> wrote:

> John,
>
> Please see below for the VMD output. The crash only seems to happen with
> one of my custom materials on a quicksurf (Other drawing methods not
> tested). I tested materials that use either a transparency or mirror, as
> well as a material that uses both. It only seems to crash for the material
> that uses both. I can provide the pdb and vis state files privately if you
> like.
>
>
> Driver version 461.09
>
>
> If you are able to estimate that perhaps it does require more than the 2
> GB of dedicated memory, I can test sometime in the next week on a 4 GB 970
> desktop. The 960M system does currently have relatively low avail system
> memory, but I can't free it up just yet.
>
>
>
> Apologies to Nikhil for taking over your thread a little.
>
>
>
> ===================================================================
>
> Info) VMD for WIN64, version 1.9.4a51 (December 21, 2020)
> 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, 8 CPUs detected.
> Info) CPU features: SSE2 SSE4.1 AVX AVX2 FMA F16 HT
> Info) Free system memory: 6349MB (38%)
> Info) Creating CUDA device pool and initializing hardware...
> CUDA error: invalid device symbol,
> C:/Users/johns/Desktop/build/vmd/src/CUDAClearDevice.cu line 54
> Info) Unable to load NVML library, GPU-CPU affinity unavailable.
> Info) Detected 1 available CUDA accelerator::
> Info) [0] GeForce GTX 960M 5 SM_5.0 1.2 GHz, 2.0GB RAM SP32 KT AE4 ZC
> Info) OpenGL renderer: GeForce GTX 960M/PCIe/SSE2
> Info) Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVFGS)
> Info) Full GLSL rendering mode is available.
> Info) Textures: 2-D (16384x16384), 3-D (2048x2048x2048), Multitexture (4)
> Info) No joysticks found. Joystick interface disabled.
> Info) Detected 1 available TachyonL/OptiX ray tracing accelerator
> Info) Compiling OptiX shaders on 1 target GPU...
> Info) Dynamically loaded 76 plugins in directory:
> Info) C:/Program Files/VMD/plugins/WIN64/molfile
> vmd > Info) Using plugin pdb for structure file C:/Users/Jason
> Smith/OneDrive/COVID-19/Notes on Communication (papers in production)/5RFA
> 1187.pdb
> Info) Using plugin pdb for coordinates from file C:/Users/Jason
> Smith/OneDrive/COVID-19/Notes on Communication (papers in production)/5RFA
> 1187.pdb
> Info) Determining bond structure from distance search ...
> Info) Eliminating bonds duplicated from existing structure...
> Info) Finished with coordinate file C:/Users/Jason
> Smith/OneDrive/COVID-19/Notes on Communication (papers in production)/5RFA
> 1187.pdb.
> Info) Analyzing structure ...
> Info) Atoms: 5388
> Info) Bonds: 4807
> Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
> Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
> Info) Residues: 1294
> Info) Waters: 683
> Info) Segments: 1
> Info) Fragments: 694 Protein: 2 Nucleic: 0
> 0
> Info) In any publication of scientific results based in part or
> Info) completely on the use of the program STRIDE, please reference:
> Info) Frishman,D & Argos,P. (1995) Knowledge-based secondary structure
> Info) assignment. Proteins: structure, function and genetics, 23, 566-579.
> CUDA Thrust sort_by_key() failed:
> C:/Users/johns/Desktop/build/vmd/src/CUDASort.cu line 190
> dev_radix_sort_by_key() failed:
> C:/Users/johns/Desktop/build/vmd/src/CUDASpatialSearch.cu line 259
> CUDA Thrust sort_by_key() failed:
> C:/Users/johns/Desktop/build/vmd/src/CUDASort.cu line 190
> dev_radix_sort_by_key() failed:
> C:/Users/johns/Desktop/build/vmd/src/CUDASpatialSearch.cu line 259
> {{1 0 0 3.883} {0 1 0 2.328} {0 0 1 -9.474} {0 0 0 1}} {{0.465909
> 0.0444488 0.88373 0} {-0.848048 0.307467 0.431632 0} {-0.252536 -0.950541
> 0.18095 0} {0 0 0 1}} {{0.0692238 0 0 0} {0 0.0692238 0 0} {0 0 0.0692238
> 0} {0 0 0 1}} {{1 0 0 0.017413} {0 1 0 -0.049682} {0 0 1 0.485529} {0 0 0
> 1}}
> 0
> 0
> CUDA Thrust sort_by_key() failed:
> C:/Users/johns/Desktop/build/vmd/src/CUDASort.cu line 190
> dev_radix_sort_by_key() failed:
> C:/Users/johns/Desktop/build/vmd/src/CUDASpatialSearch.cu line 259
> Info) Rendering current scene to 'vmdscene.ppm' ...
> OptiXDisplayDevice) Total rendering time: 0.72 sec
> Info) Executing post-render cmd 'explorer vmdscene.ppm' ...
> Info) Rendering complete.
> Info) Rendering current scene to 'vmdscene.ppm' ...
> OptiXDisplayDevice) Total rendering time: 0.34 sec
> Info) Executing post-render cmd 'explorer vmdscene.ppm' ...
> Info) Rendering complete.
> Info) Rendering current scene to 'vmdscene.ppm' ...
> ERROR) OptiXRenderer) ERROR: Unknown error (Details: Function
> "_rtContextLaunch2D" caught exception: Encountered a CUDA error:
> cudaDriver().CuEventSynchronize( m_event ) returned (702): Launch timeout,
> file: <internal>, line: 0)
> (c:\users\johns\desktop\build\vmd\src\optixrenderer.c:4969
> ERROR) OptiXRenderer) ERROR: Unknown error (Details: Function
> "_rtContextLaunch2D" caught exception: Assertion failed: "!m_launching :
> Memory manager launch is already active", file: <internal>, line: 1103)
> (c:\users\johns\desktop\build\vmd\src\optixrenderer.c:4975
> OptiXRenderer) Error during rendering. Rendering aborted.
> ERROR) OptiXRenderer) ERROR: Unknown error (Details: Function
> "_rtAccelerationDestroy" caught exception: Assertion failed:
> "!m_launching", file: <internal>, line: 211)
> (c:\users\johns\desktop\build\vmd\src\optixrenderer.c:1426
> ERROR) OptiXRenderer) ERROR: Unknown error (Details: Function
> "_rtAccelerationDestroy" caught exception: Assertion failed:
> "!m_launching", file: <internal>, line: 211)
> (c:\users\johns\desktop\build\vmd\src\optixrenderer.c:1429
> ERROR) OptiXRenderer) ERROR: Unknown error (Details: Function
> "_rtAccelerationDestroy" caught exception: Assertion failed:
> "!m_launching", file: <internal>, line: 211)
> (c:\users\johns\desktop\build\vmd\src\optixrenderer.c:1432
> ERROR) OptiXRenderer) ERROR: Unknown error (Details: Function
> "_rtGroupDestroy" caught exception: Assertion failed: "!m_launching", file:
> <internal>, line: 211)
> (c:\users\johns\desktop\build\vmd\src\optixrenderer.c:1433
>
>
>
>
>
> Cheers,
> -
> Jason Smith
> Post-Doctoral Fellow
> Robert N. Young Lab, Simon Fraser University
> 8888 University Drive, Burnaby, BC, V5A-1S6
> Canada
>
> ------------------------------
> *From:* John Stone <johns_at_ks.uiuc.edu>
> *Sent:* Thursday, 15 April 2021 9:38:02 AM
> *To:* Jason Smith
> *Cc:* Geist, Norman; Nikhil Maroli; Vmd L
> *Subject:* Re: vmd-l: Rendering using GPU
>
> Jason,
> There shouldn't be crashes on the older GPUs, even with things like
> mirror reflection being used. It's possible that on a 960M one might
> run short on GPU memory, but I'm still surprised you're getting a crash.
> What driver version are you running on that machine? Does VMD print any
> errors when this crash you've described occurs?
>
> Best,
> John Stone
>
> On Thu, Apr 15, 2021 at 04:26:05PM +0000, Jason Smith wrote:
> > My Apologies,
> >
> > I just tested 1.9.4a51v6 on a 960M (while John was writing his reply)
> and
> > both in-memory and interactive tachyon-optix works fine, so long as
> you
> > aren't attempting to use RT-based effects like mirror (which leads to
> a
> > crash-to-desktop).
> >
> > Cheers,
> >
> > -
> > Jason Smith
> > Post-Doctoral Fellow
> > Robert N. Young Lab, Simon Fraser University
> > 8888 University Drive, Burnaby, BC, V5A-1S6
> > Canada
> >
> >
> --------------------------------------------------------------------------
> >
> > From: Jason Smith
> > Sent: Thursday, 15 April 2021 9:08:29 AM
> > To: John Stone; Geist, Norman
> > Cc: Nikhil Maroli; Vmd L
> > Subject: Re: vmd-l: Rendering using GPU
> >
> >
> > Correct me if I'm wrong, but ray tracing with Optix requires the ray
> > tracing cores present on 2000 and later series NVidia GPUs.
> >
> > Cheers,
> >
> > -
> > Jason Smith
> > Post-Doctoral Fellow
> > Robert N. Young Lab, Simon Fraser University
> > 8888 University Drive, Burnaby, BC, V5A-1S6
> > Canada
> >
> >
> --------------------------------------------------------------------------
> >
> > From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of
> John
> > Stone <johns_at_ks.uiuc.edu>
> > Sent: Thursday, 15 April 2021 8:20:42 AM
> > To: Geist, Norman
> > Cc: Nikhil Maroli; Vmd L
> > Subject: Re: vmd-l: Rendering using GPU
> >
> > Hi,
> > When VMD starts up, it automatically detects NVIDIA GPUs
> > that support CUDA and OptiX (OptiX is the ray tracing development
> > framework I used to write the existing lightegith GPU version of
> Tachyon).
> > If you've got up-to-date NVIDIA drivers, you should see a VMD startup
> > message
> > that looks similar to this:
> >
> > Info) Detected 3 available TachyonL/OptiX ray tracing accelerators
> > Info) Compiling OptiX shaders on 3 target GPUs...
> >
> > If no OptiX-capable GPUs are seen by VMD, then you won't see the
> > various "TachyonL-OptiX" renderers listed in in the File->Render menu.
> >
> > Best regards,
> > John Stone
> >
> > On Thu, Apr 15, 2021 at 10:45:48AM +0200, Geist, Norman wrote:
> > > Use renderers with optix in their names.
> > >
> > > Am Donnerstag, den 15-04-2021 um 09:31 schrieb Nikhil Maroli:
> > >
> > > Dear All,
> > > I am having 3 x 1070 with a 2 x 12 core processor. I have
> > installed VMD
> > > for CUDA versions. When I load VMD I can see it uses 700Mb
> from the
> > > card, however rendering always running on the processor.
> > > Can anyone tell me how I use cards for rendering purposes
> > > Nikhil
> > > --
> >
> > --
> > NIH Center for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > [1]http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> > [2]http://www.ks.uiuc.edu/Research/vmd/
> >
> > References
> >
> > Visible links
> > 1. http://www.ks.uiuc.edu/~johns/
> > 2. 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/
>