VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 16 2019 - 17:28:15 CDT

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/ 

-- 
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/