From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Dec 13 2019 - 00:09:20 CST

Dallas,
  I've been testing OptiX 6.5.0 with driver version 440.44,
and it seems that the problem I'd previously experienced with
a runtime crash during deallocation of geometry instance objects
now appears to be cured. I will have to significantly more testing
tomorrow, but if it all goes well, then I can finally eliminate the
workaround I put into VMD (which is the cause of the leak you had
experienced) can finally be eliminated.

If you're game to try a new test build, I can probably make one available
tomorrow sometime after I do more testing.

Best,
  John

On Fri, Nov 15, 2019 at 08:41:48AM +1100, Dallas Warren wrote:
> vmd 1.9.4a38
> Driver Version: 440.31
> CUDA Version: 10.2
> GeForce RTX 2080 Ti
> 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 Fri, 15 Nov 2019 at 08:35, Dallas Warren <[2]dallas.warren_at_monash.edu>
> wrote:
>
> I noticed that you posted a new alpha a little while ago, so I have
> installed 1.9.4a38
> Testing with rendering of a movie with TachyonL-OptiX there still exists
> a memory leak. It is not as significant as it was, it creeps up much
> more slowly. But still eventually overflows.
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> [3]dallas.warren_at_monash.edu
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble
> a nail.
> On Wed, 24 Jul 2019 at 14:28, John Stone <[4]johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> ¬ I've reproduced the problem with the NORTX mode of VMD.¬
> I'm personally convinced this is a bug within either
> the specific video driver versions where it occurs, as
> it has previously worked fine with other driver versions
> with no other changes to the code.¬ The error messages are from deep
> inside the just-in-time (JIT) compilation phase of the OptiX runtime,
> and they arise from code that isn't in the PTX resulting from
> compilation
> of the VMD OptiX shaders, as there are no shuffle instructions in
> the VMD code.¬ I expect to meet up with members of the OptiX team
> next week at Siggraph, and I may be able to demonstrate the issue
> for them while I'm there.
>
> In the mean time, I'm working on another fix for the issues that
> still remain in the RTX-enabled rendering path due to what I believe
> is recursion in excess of what OptiX permits.
> I know about the leak issue, and that should be cured once I've
> got the recursion issue solved.
>
> Best,
> ¬ John Stone
> ¬ [5]vmd_at_ks.uiuc.edu
>
> On Fri, Jul 19, 2019 at 11:11:33AM +0200, Michael Gecht wrote:
> > 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) [6]http://www.ks.uiuc.edu/Research/vmd/
> > Info) Email questions and bug reports to [7]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][8]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][9]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) [3][10]http://www.ks.uiuc.edu/Research/vmd/ √*¬
> √*¬ √*¬ √*¬ √*¬ √*¬ √*¬ √*¬ √*
> > >>¬ ¬ ¬ √*¬ √*¬ √*
> > >>¬ ¬ ¬ Info) Email questions and bug reports to
> [4][11]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
> > >>¬ ¬ ¬ [5][12]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][13]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
> > >>¬ ¬ ¬ ¬ √*¬ [7][14]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][15]http://www.ks.uiuc.edu/~johns/√*¬ √*¬ √*¬
> √*¬ √*¬ √* Phone: 217-244-3349
> > >>¬ ¬ ¬ ¬ [9][16]http://www.ks.uiuc.edu/Research/vmd/√*¬ √*¬
> √*
> > >>
> > >>References
> > >>
> > >>¬ ¬ Visible links
> > >>¬ ¬ 1. mailto:[17]dallas.warren_at_monash.edu
> > >>¬ ¬ 2. mailto:[18]dallas.warren_at_monash.edu
> > >>¬ ¬ 3. [19]http://www.ks.uiuc.edu/Research/vmd/
> > >>¬ ¬ 4. mailto:[20]vmd_at_ks.uiuc.edu
> > >>¬ ¬ 5. mailto:[21]dallas.warren_at_monash.edu
> > >>¬ ¬ 6. mailto:[22]johns_at_ks.uiuc.edu
> > >>¬ ¬ 7. mailto:[23]vmd_at_ks.uiuc.edu
> > >>¬ ¬ 8. [24]http://www.ks.uiuc.edu/~johns/
> > >>¬ ¬ 9. [25]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
> [26]http://www.ks.uiuc.edu/~johns/¬ ¬ ¬ ¬ ¬ ¬ Phone: 217-244-3349
> [27]http://www.ks.uiuc.edu/Research/vmd/¬ ¬ ¬
>
> References
>
> Visible links
> 1. mailto:dallas.warren_at_monash.edu
> 2. mailto:dallas.warren_at_monash.edu
> 3. mailto:dallas.warren_at_monash.edu
> 4. mailto:johns_at_ks.uiuc.edu
> 5. mailto:vmd_at_ks.uiuc.edu
> 6. http://www.ks.uiuc.edu/Research/vmd/
> 7. mailto:vmd_at_ks.uiuc.edu
> 8. mailto:dallas.warren_at_monash.edu
> 9. mailto:dallas.warren_at_monash.edu
> 10. http://www.ks.uiuc.edu/Research/vmd/
> 11. mailto:vmd_at_ks.uiuc.edu
> 12. mailto:dallas.warren_at_monash.edu
> 13. mailto:johns_at_ks.uiuc.edu
> 14. mailto:vmd_at_ks.uiuc.edu
> 15. http://www.ks.uiuc.edu/~johns/%C3%82
> 16. http://www.ks.uiuc.edu/Research/vmd/%C3%82
> 17. mailto:dallas.warren_at_monash.edu
> 18. mailto:dallas.warren_at_monash.edu
> 19. http://www.ks.uiuc.edu/Research/vmd/
> 20. mailto:vmd_at_ks.uiuc.edu
> 21. mailto:dallas.warren_at_monash.edu
> 22. mailto:johns_at_ks.uiuc.edu
> 23. mailto:vmd_at_ks.uiuc.edu
> 24. http://www.ks.uiuc.edu/~johns/
> 25. http://www.ks.uiuc.edu/Research/vmd/
> 26. http://www.ks.uiuc.edu/~johns/
> 27. 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/