VMD-L Mailing List

From: Michael Gecht (michael.gecht_at_biophys.mpg.de)
Date: Fri Jul 19 2019 - 04:11:33 CDT

Dear John,

I am also experiencing problems with the current alpha on RTX 2070 cards
(Driver Version: 430.34, CUDA Version: 10.1). Initial rendering works,
but starts to fail after a few (dozen) frames. With the VMDOPTIXNORTX
environment variable set before starting VMD, I am unable to render even
one single frame with TachyonL-OptiX. VMD startup log + crash message below.

Best,
Michael

migecht_at_workstation:frame3802$ export VMDOPTIXNORTX=1
migecht_at_workstation:frame3802$ vmdar -e viewmaster-session.vmd
Info) VMD for LINUXAMD64, version 1.9.4a35 (July 10, 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, 8 CPUs detected.
Info)   CPU features: SSE2 AVX AVX2 FMA AVX512F AVX512CD
Info) Free system memory: 56GB (89%)
Info) Creating CUDA device pool and initializing hardware...
Info) Detected 1 available CUDA accelerator::
Info) [0] GeForce RTX 2070     36 SM_7.5 1.6 GHz, 7.8GB RAM SP32 KT AE3 ZC
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 2070/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) /home/tb/migecht/.lib/vmdar/plugins/LINUXAMD64/molfile
after#0
2.6
Info) Using plugin pdb for structure file
/<redacted>/migecht/DATA/projects/<redacted>/render/frame3802/frame3802.pdb
Info) Using plugin pdb for coordinates from file
/STORAGE/migecht/DATA/projects/<redacted>/render/frame3802/frame3802.pdb
Info) Determining bond structure from distance search ...
Info) Finished with coordinate file
/<redacted>/migecht/DATA/projects/<redacted>/render/frame3802/frame3802.pdb.
Info) Analyzing structure ...
Info)    Atoms: 98926
Info)    Bonds: 78052
Info)    Angles: 0  Dihedrals: 0  Impropers: 0  Cross-terms: 0
Info)    Bondtypes: 0  Angletypes: 0  Dihedraltypes: 0 Impropertypes: 0
Info)    Residues: 21066
Info)    Waters: 20502
Info)    Segments: 1
Info)    Fragments: 20916   Protein: 3   Nucleic: 0
Info) Using plugin xtc for coordinates from file
/<redacted>/migecht/DATA/projects/<redacted>/render/frame3802/traj.xtc
Info) Finished with coordinate file
/<redacted>/migecht/DATA/projects/<redacted>/render/frame3802/traj.xtc.
vmd > 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.
Info) Rendering current scene to 'vmdscene.ppm' ...
Info) Ambient occlusion enabled.
Info) Shadow rendering enabled.
ERROR) OptiXRenderer) ERROR: Unknown error (Details: Function "RTresult
_rtContextLaunch2D(RTcontext, unsigned int, RTsize, RTsize)" caught
exception: Encountered a CUDA error: ptxas application ptx input, line
59; error   : Feature 'activemask' requires PTX ISA .version 6.2 or later
ERROR) ptxas application ptx input, line 62; error   : Feature
'shfl.sync' requires PTX ISA .version 6.0 or later
ERROR) ptxas application ptx input, line 65; error   : Feature
'shfl.sync' requires PTX ISA .version 6.0 or later
ERROR) ptxas application ptx input, line 68; error   : Feature
'shfl.sync' requires PTX ISA .version 6.0 or later
ERROR) ptxas application ptx input, line 71; error   : Feature
'shfl.sync' requires PTX ISA .version 6.0 or later
ERROR) ptxas application ptx input, line 74; error   : Feature
'shfl.sync' requires PTX ISA .version 6.0 or later
ERROR) ptxas application ptx input, line 1209; error   : Feature
'shfl.sync' requires PTX ISA .version 6.0 or later
ERROR) ptxas application ptx input, line 1471; error   : Feature
'shfl.sync' requires PTX ISA .version 6.0 or later
ERROR) ptxas application ptx input, line 1473; error   : Feature
'shfl.sync' requires PTX ISA .version 6.0 or later
ERROR) ptxas application ptx input, line 1475; error   : Feature
'shfl.sync' requires PTX ISA .version 6.0 or later
ERROR) ptxas application ptx input, line 1477; error   : Feature
'shfl.sync' requires PTX ISA .version 6.0 or later
ERROR) ptxas application ptx input, line 1479; error   : Feature
'shfl.sync' requires PTX ISA .version 6.0 or later
OptiXRenderer) Creating OptiX window: 1762 x 1341...
OptiXRenderer) VMD TachyonL-OptiX Interactive Ray Tracer help:
OptiXRenderer) ===============================================
OptiXRenderer) Using 1 device:
OptiXRenderer) [0] GeForce RTX 2070     CUDA[0], 7.8GB RAM, KTO
OptiXRenderer)
OptiXRenderer) Spaceball/SpaceNavigator/Magellan: Not available
OptiXRenderer) Stereoscopic display: Not available
OptiXRenderer) Vert retrace sync: On
OptiXRenderer)
OptiXRenderer) General controls:
OptiXRenderer)   space: save numbered snapshot image
OptiXRenderer)       =: reset to initial view
OptiXRenderer)       h: print this help info
OptiXRenderer)       p: print current rendering parameters
OptiXRenderer)   ESC,q: quit viewer
OptiXRenderer)
OptiXRenderer) Display controls
OptiXRenderer)      F1: override shadows on/off (off=AO off too)
OptiXRenderer)      F2: override AO on/off
OptiXRenderer)      F3: override DoF on/off
OptiXRenderer)      F4: override Depth cueing on/off
OptiXRenderer)     F12: toggle full-screen display on/off
OptiXRenderer)   1-9,0: override samples per update auto-FPS off
OptiXRenderer)      Up: increase DoF focal distance
OptiXRenderer)    Down: decrease DoF focal distance
OptiXRenderer)    Left: decrease DoF f/stop
OptiXRenderer)   Right: increase DoF f/stop
OptiXRenderer)       S: toggle stereoscopic display on/off (if avail)
OptiXRenderer)       a: toggle AA/AO auto-FPS tuning on/off (on)
OptiXRenderer)       g: toggle gradient sky xforms on/off (on)
OptiXRenderer)       l: toggle light xforms on/off (on)
OptiXRenderer)
OptiXRenderer) Mouse controls:
OptiXRenderer)       f: mouse depth-of-field mode
OptiXRenderer)       r: mouse rotation mode
OptiXRenderer)       s: mouse scaling mode
OptiXRenderer)       t: mouse translation mode
OptiXRenderer) An error occured in AS generation. Rendering is aborted.

OptiXDisplayDevice) Total rendering time: 0.59 sec
Info) Executing post-render cmd 'display vmdscene.ppm' ...
display: improper image header `vmdscene.ppm' @
error/pnm.c/ReadPNMImage/293.
Info) Rendering complete.

On 17/07/19 00:28, John Stone wrote:
> Dallas,
> I'm aware of the issue, for the moment try setting this environment
> variable before running VMD as a workaround until the next beta.
> I'm still chasing this bug and another related issue.
> bash
> export VMDOPTIXNORTX=1
> csh:
> setenv VMDOPTIXNORTX 1
>
> Best,
> John
>
> On Wed, Jul 17, 2019 at 08:18:16AM +1000, Dallas Warren wrote:
>> Note I think it is actually only CUDA 10.1, only place can find 10.2
>> mentioned is from the nvidia-smi call, and can't find any mention of 10.2
>> existing online.
>> Catch ya,
>>
>> Dr. Dallas Warren
>> Drug Delivery, Disposition and Dynamics
>> Monash Institute of Pharmaceutical Sciences, Monash University
>> 381 Royal Parade, Parkville VIC 3052
>> [1]dallas.warren_at_monash.edu
>> ---------------------------------
>> When the only tool you own is a hammer, every problem begins to resemble a
>> nail.
>> On Mon, 15 Jul 2019 at 11:10, Dallas Warren <[2]dallas.warren_at_monash.edu>
>> wrote:
>>
>> John,
>> I'm still getting a memory leak with 1.9.4a35 and image rendering
>> (TachyonL-OptiX) using an RTX2080Ti card, driver 430.26, CUDA 10.2
>> I obtained the same issue with a31, but does not occur with a8 which is
>> what I am having to use currently.
>> Below I have output from nvidia-smi before and after a rendering step
>> and post failure, vmd output when error occurs, and the start up output
>> from vmd.
>> Let me know if there is any further information I can provide to assist.
>> ######################################
>> Here are two nvidia-smi calls before and after a rendering using the
>> movie extension, memory used creeps up with each rendered frame/image.
>> dallas_at_morph:~> nvidia-smi
>> Mon Jul 15 10:51:45 2019 Â Â Â
>> +-----------------------------------------------------------------------------+
>> | NVIDIA-SMI 430.26 Â Â Â Driver Version: 430.26 Â Â Â CUDA
>> Version: 10.2 Â Â |
>> |-------------------------------+----------------------+----------------------+
>> | GPU  Name     Persistence-M| Bus-Id     Disp.A |
>> Volatile Uncorr. ECC |
>> | Fan  Temp  Perf  Pwr:Usage/Cap|     Memory-Usage | GPU-Util
>> Â Compute M. |
>> |===============================+======================+======================|
>> |  0  GeForce RTX 208... Off  | 00000000:02:00.0  On |   Â
>> Â Â Â Â Â Â N/A |
>> | 28% Â 55C Â Â P2 Â 266W / 260W | Â 5525MiB / 11011MiB | Â Â 10%
>> Â Â Â Default |
>> +-------------------------------+----------------------+----------------------+
>> Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â
>> Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â
>> +-----------------------------------------------------------------------------+
>> | Processes: Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â
>> Â Â Â Â Â Â Â GPU Memory |
>> |  GPU    PID  Type  Process name         Â
>>      Usage    |
>> |=============================================================================|
>> | Â Â 0 Â Â Â 2413 Â Â Â G Â /usr/bin/X Â Â Â Â Â Â Â Â Â
>> Â Â Â Â Â Â Â Â 183MiB |
>> | Â Â 0 Â Â Â 2922 Â Â Â G Â kwin_x11 Â Â Â Â Â Â Â Â Â
>> Â Â Â Â Â Â Â Â Â Â 29MiB |
>> |   0    2926    G  /usr/bin/krunner       Â
>> Â Â Â Â Â Â Â Â 6MiB |
>> |   0    2931    G  /usr/bin/plasmashell     Â
>> Â Â Â Â Â Â Â Â 73MiB |
>> | Â Â 0 Â Â Â 3564 Â Â C+G Â
>> /usr/local/lib/vmd_1.9.4a35/vmd_LINUXAMD64 Â 5227MiB |
>> +-----------------------------------------------------------------------------+
>> dallas_at_morph:~> nvidia-smi
>> Mon Jul 15 10:51:49 2019 Â Â Â
>> +-----------------------------------------------------------------------------+
>> | NVIDIA-SMI 430.26 Â Â Â Driver Version: 430.26 Â Â Â CUDA
>> Version: 10.2 Â Â |
>> |-------------------------------+----------------------+----------------------+
>> | GPU  Name     Persistence-M| Bus-Id     Disp.A |
>> Volatile Uncorr. ECC |
>> | Fan  Temp  Perf  Pwr:Usage/Cap|     Memory-Usage | GPU-Util
>> Â Compute M. |
>> |===============================+======================+======================|
>> |  0  GeForce RTX 208... Off  | 00000000:02:00.0  On |   Â
>> Â Â Â Â Â Â N/A |
>> | 27% Â 57C Â Â P2 Â 250W / 260W | Â 5645MiB / 11011MiB | Â Â 37%
>> Â Â Â Default |
>> +-------------------------------+----------------------+----------------------+
>> Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â
>> Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â
>> +-----------------------------------------------------------------------------+
>> | Processes: Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â
>> Â Â Â Â Â Â Â GPU Memory |
>> |  GPU    PID  Type  Process name         Â
>>      Usage    |
>> |=============================================================================|
>> | Â Â 0 Â Â Â 2413 Â Â Â G Â /usr/bin/X Â Â Â Â Â Â Â Â Â
>> Â Â Â Â Â Â Â Â 183MiB |
>> | Â Â 0 Â Â Â 2922 Â Â Â G Â kwin_x11 Â Â Â Â Â Â Â Â Â
>> Â Â Â Â Â Â Â Â Â Â 29MiB |
>> |   0    2926    G  /usr/bin/krunner       Â
>> Â Â Â Â Â Â Â Â 6MiB |
>> |   0    2931    G  /usr/bin/plasmashell     Â
>> Â Â Â Â Â Â Â Â 73MiB |
>> | Â Â 0 Â Â Â 3564 Â Â C+G Â
>> /usr/local/lib/vmd_1.9.4a35/vmd_LINUXAMD64 Â 5347MiB |
>> +-----------------------------------------------------------------------------+
>> ######################################
>> Post failure:
>> dallas_at_morph:~> nvidia-smi
>> Mon Jul 15 10:56:30 2019 Â Â Â
>> +-----------------------------------------------------------------------------+
>> | NVIDIA-SMI 430.26 Â Â Â Driver Version: 430.26 Â Â Â CUDA
>> Version: 10.2 Â Â |
>> |-------------------------------+----------------------+----------------------+
>> | GPU  Name     Persistence-M| Bus-Id     Disp.A |
>> Volatile Uncorr. ECC |
>> | Fan  Temp  Perf  Pwr:Usage/Cap|     Memory-Usage | GPU-Util
>> Â Compute M. |
>> |===============================+======================+======================|
>> |  0  GeForce RTX 208... Off  | 00000000:02:00.0  On |   Â
>> Â Â Â Â Â Â N/A |
>> | 24% Â 39C Â Â P8 Â Â 29W / 260W | Â 10936MiB / 11011MiB | Â Â
>> Â 2% Â Â Â Default |
>> +-------------------------------+----------------------+----------------------+
>> Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â
>> Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â
>> +-----------------------------------------------------------------------------+
>> | Processes: Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â
>> Â Â Â Â Â Â Â GPU Memory |
>> |  GPU    PID  Type  Process name         Â
>>      Usage    |
>> |=============================================================================|
>> | Â Â 0 Â Â Â 2413 Â Â Â G Â /usr/bin/X Â Â Â Â Â Â Â Â Â
>> Â Â Â Â Â Â Â Â 214MiB |
>> | Â Â 0 Â Â Â 2922 Â Â Â G Â kwin_x11 Â Â Â Â Â Â Â Â Â
>> Â Â Â Â Â Â Â Â Â Â 31MiB |
>> |   0    2926    G  /usr/bin/krunner       Â
>> Â Â Â Â Â Â Â Â 6MiB |
>> |   0    2931    G  /usr/bin/plasmashell     Â
>> Â Â Â Â Â Â Â Â 73MiB |
>> | Â Â 0 Â Â Â 3564 Â Â C+G Â
>> /usr/local/lib/vmd_1.9.4a35/vmd_LINUXAMD64 10605MiB |
>> +-----------------------------------------------------------------------------+
>> ######################################
>> vmd output at the point at which it fails:
>> Info) Rendering current scene to
>> '/home/dallas/Pictures/vmd/5_md_001_rotation.00067.ppm' ...
>> Info) Ambient occlusion enabled.
>> Info) Shadow rendering enabled.
>> OptiXDisplayDevice) Total rendering time: 2.86 sec
>> Info) Rendering complete.
>> Info) Rendering current scene to
>> '/home/dallas/Pictures/vmd/5_md_001_rotation.00068.ppm' ...
>> Info) Ambient occlusion enabled.
>> Info) Shadow rendering enabled.
>> ERROR) OptiXRenderer) ERROR: Memory allocation failed (Details: Function
>> "RTresult _rtContextLaunch2D(RTcontext, unsigned int, RTsize, RTsize)"
>> caught exception: Out of memory) (OptiXRenderer.C:2621
>> OptiXRenderer) Error during AS generation. Rendering aborted.
>> OptiXDisplayDevice) Total rendering time: 0.32 sec
>> Info) Rendering complete.
>> ######################################
>> vmd start up output:
>> dallas_at_morph:~/Pictures/vmd> vmd_1.9.4a35
>> /usr/local/lib/vmd_1.9.4a35/vmd_LINUXAMD64: /usr/lib64/libGL.so.1: no
>> version information available (required by
>> /usr/local/lib/vmd_1.9.4a35/vmd_LINUXAMD64)
>> Info) VMD for LINUXAMD64, version 1.9.4a35 (July 10, 2019)
>> Info) [3]http://www.ks.uiuc.edu/Research/vmd/ Â Â Â Â Â Â Â Â Â
>> Â Â Â
>> Info) Email questions and bug reports to [4]vmd_at_ks.uiuc.edu    Â
>> Â
>> Info) Please include this reference in published work using VMD: Â
>> Info) Â Â Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual Â
>> Info) Â Â Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
>> Info) -------------------------------------------------------------
>> Info) Multithreading available, 12 CPUs detected.
>> Info) Â CPU features: SSE2 AVX
>> Info) Free system memory: 33GB (93%)
>> Info) Creating CUDA device pool and initializing hardware...
>> Info) Detected 1 available CUDA accelerator::
>> Info) [0] GeForce RTX 2080 Ti  68 SM_7.5 1.6 GHz, 11GB RAM SP32 KT AE3
>> ZC
>> 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) Â Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVFGS)
>> Info) Â Full GLSL rendering mode is available.
>> Info) Â Textures: 2-D (32768x32768), 3-D (16384x16384x16384),
>> Multitexture (4)
>> Info) Detected 1 available TachyonL/OptiX ray tracing accelerator
>> Info) Â Compiling 1 OptiX shaders on 1 target GPU...
>> Info) Dynamically loaded 3 plugins in directory:
>> Info) /usr/local/lib/vmd_1.9.4a35/plugins/LINUXAMD64/molfile
>> after#0
>> Catch ya,
>>
>> Dr. Dallas Warren
>> Drug Delivery, Disposition and Dynamics
>> Monash Institute of Pharmaceutical Sciences, Monash University
>> 381 Royal Parade, Parkville VIC 3052
>> [5]dallas.warren_at_monash.edu
>> ---------------------------------
>> When the only tool you own is a hammer, every problem begins to resemble
>> a nail.
>> On Thu, 11 Jul 2019 at 07:29, John Stone <[6]johns_at_ks.uiuc.edu> wrote:
>>
>> Hi,
>> Â I've just posted two new Linux and MacOS X test binaries
>> of VMD 1.9.4 alpha 35. The new version includes new structure
>> building plugins, a new colvars dashboard tool, updates to the
>> RTX-accelerated ray tracing engines to quash one of the
>> outstanding bugs that people had run into with previous builds.
>>
>> I expect that we will begin a more rapid update cycle soon because
>> we have also made some massive updates to VMD's Python support with
>> contributions from Robin Betz and others, and I'm looking for a
>> good way to redistribute pre-built VMD binaries that are linked
>> against the latest Python 3.x versions.
>>
>> We will have alpha builds for other platforms (various Windows and
>> 64-bit MacOS X) starting to become available as bugs get reported
>> and quashed in the new plugins.
>>
>> Some of the contributors to the new tools in this beta will
>> followup on this email with specifics of the new features/tools
>> they've added for those eager to try them out.
>>
>> Best regards,
>> Â John Stone
>> Â [7]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
>> [8]http://www.ks.uiuc.edu/~johns/Â Â Â Â Â Â Phone: 217-244-3349
>> [9]http://www.ks.uiuc.edu/Research/vmd/Â Â Â
>>
>> References
>>
>> Visible links
>> 1. mailto:dallas.warren_at_monash.edu
>> 2. mailto:dallas.warren_at_monash.edu
>> 3. http://www.ks.uiuc.edu/Research/vmd/
>> 4. mailto:vmd_at_ks.uiuc.edu
>> 5. mailto:dallas.warren_at_monash.edu
>> 6. mailto:johns_at_ks.uiuc.edu
>> 7. mailto:vmd_at_ks.uiuc.edu
>> 8. http://www.ks.uiuc.edu/~johns/
>> 9. http://www.ks.uiuc.edu/Research/vmd/