VMD-L Mailing List

From: Dallas Warren (dallas.warren_at_monash.edu)
Date: Sun Jul 14 2019 - 20:10:43 CDT

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/
>
>