From: Dallas Warren (dallas.warren_at_monash.edu)
Date: Tue Jul 16 2019 - 17:18:16 CDT

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
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 <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
>
> +-----------------------------------------------------------------------------+
> | NVIDIA-SMI 430.26 Driver Version: 430.26 CUDA Version: 10.2
> |
>
> |-------------------------------+----------------------+----------------------+
> | GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr.
> ECC |
> | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute
> M. |
>
> |===============================+======================+======================|
> | 0 GeForce RTX 208... Off | 00000000:02:00.0 On |
> N/A |
> | 28% 55C P2 266W / 260W | 5525MiB / 11011MiB | 10%
> Default |
>
> +-------------------------------+----------------------+----------------------+
>
>
>
> +-----------------------------------------------------------------------------+
> | Processes: GPU
> Memory |
> | GPU PID Type Process name Usage
> |
>
> |=============================================================================|
> | 0 2413 G /usr/bin/X
> 183MiB |
> | 0 2922 G kwin_x11
> 29MiB |
> | 0 2926 G /usr/bin/krunner
> 6MiB |
> | 0 2931 G /usr/bin/plasmashell
> 73MiB |
> | 0 3564 C+G /usr/local/lib/vmd_1.9.4a35/vmd_LINUXAMD64
> 5227MiB |
>
> +-----------------------------------------------------------------------------+
> dallas_at_morph:~> nvidia-smi
> Mon Jul 15 10:51:49 2019
>
> +-----------------------------------------------------------------------------+
> | NVIDIA-SMI 430.26 Driver Version: 430.26 CUDA Version: 10.2
> |
>
> |-------------------------------+----------------------+----------------------+
> | GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr.
> ECC |
> | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute
> M. |
>
> |===============================+======================+======================|
> | 0 GeForce RTX 208... Off | 00000000:02:00.0 On |
> N/A |
> | 27% 57C P2 250W / 260W | 5645MiB / 11011MiB | 37%
> Default |
>
> +-------------------------------+----------------------+----------------------+
>
>
>
> +-----------------------------------------------------------------------------+
> | Processes: GPU
> Memory |
> | GPU PID Type Process name Usage
> |
>
> |=============================================================================|
> | 0 2413 G /usr/bin/X
> 183MiB |
> | 0 2922 G kwin_x11
> 29MiB |
> | 0 2926 G /usr/bin/krunner
> 6MiB |
> | 0 2931 G /usr/bin/plasmashell
> 73MiB |
> | 0 3564 C+G /usr/local/lib/vmd_1.9.4a35/vmd_LINUXAMD64
> 5347MiB |
>
> +-----------------------------------------------------------------------------+
>
> ######################################
> Post failure:
> dallas_at_morph:~> nvidia-smi
> Mon Jul 15 10:56:30 2019
>
> +-----------------------------------------------------------------------------+
> | NVIDIA-SMI 430.26 Driver Version: 430.26 CUDA Version: 10.2
> |
>
> |-------------------------------+----------------------+----------------------+
> | GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr.
> ECC |
> | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute
> M. |
>
> |===============================+======================+======================|
> | 0 GeForce RTX 208... Off | 00000000:02:00.0 On |
> N/A |
> | 24% 39C P8 29W / 260W | 10936MiB / 11011MiB | 2%
> Default |
>
> +-------------------------------+----------------------+----------------------+
>
>
>
> +-----------------------------------------------------------------------------+
> | Processes: GPU
> Memory |
> | GPU PID Type Process name Usage
> |
>
> |=============================================================================|
> | 0 2413 G /usr/bin/X
> 214MiB |
> | 0 2922 G kwin_x11
> 31MiB |
> | 0 2926 G /usr/bin/krunner
> 6MiB |
> | 0 2931 G /usr/bin/plasmashell
> 73MiB |
> | 0 3564 C+G /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) 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: 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) 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_1.9.4a35/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
> 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 <johns_at_ks.uiuc.edu> wrote:
>
>> Hi,
>> 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,
>> 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/
>>
>>