VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Apr 10 2015 - 01:51:22 CDT

Norman,
  Have you observed anything more about the out-of-memory scenarios
that you had been running into a while back when running the interactive
GPU ray tracer in VMD? If you're still observing the same issues,
I may have a few things to ask you to try to help track it down.
Let me know.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Feb 16, 2015 at 09:23:37AM +0100, Norman Geist wrote:
> John,
>
> I've tested again with the upgraded driver, but it didn't make any
> difference.
> So I'll waiting for your updated VMD build to test.
>
> Norman Geist
>
> > -----Original Message-----
> > From: John Stone [mailto:johns_at_ks.uiuc.edu]
> > Sent: Friday, February 13, 2015 4:42 PM
> > To: Norman Geist
> > Cc: VMD Mailing List
> > Subject: Re: vmd-l: Handful of rendering issues
> >
> > Norman,
> > Okay, so "Trbvh" is breaking on your machine, at least in two
> > different
> > cases, but "MedianBvh" works. I assume your crash when rendering the
> > single sphere has also gone away. I'm currently running NVIDIA driver
> > version 346.35 and I was not able to reproduce either your crashes
> > locally, but I was testing on different GPU types than you did.
> > I know it's a hassle, but if you have time to upgrade your driver to
> > a newer version like 346.35, I'd love to know if that makes any
> > difference
> > for the problems you have reported or not. If not, then we have found
> > something amiss, most likely with the "Trbvh" builder, and we'll want
> > to
> > do further tests on this. I am beginning to test the prerelease
> > version of
> > OptiX 3.7, and it has a newer "Trbvh" builder that reportedly includes
> > some
> > more bug fixes, so I would like to have you try a new VMD build that
> > includes
> > that if possible in the next couple weeks.
> >
> > The issue with the odd appearance of the ruler is due to the emulation
> > of
> > lines with cylinders, and is expected until I have time to improve it
> > further. The line emulation in the OptiX code isn't as good as the one
> > in Tachyon yet, but I will be working on that for the next release.
> >
> > Cheers,
> > John
> >
> >
> > On Fri, Feb 13, 2015 at 04:25:36PM +0100, Norman Geist wrote:
> > > John,
> > >
> > > I've tested doing:
> > >
> > > 1. open VMD
> > > 2. disable axis
> > > 3. enable ruler
> > > 4. set env(VMDOPTIXBUILDER) "MedianBvh"
> > > 5. render using TachyonOptix
> > >
> > > This worked, although the ruler looked weirdly bended.
> > > In the same VMD session a switching to "Trbvh" again, brought
> > > the error back.
> > >
> > > Hope that helps
> > >
> > > Norman Geist
> > >
> > > > -----Original Message-----
> > > > From: John Stone [mailto:johns_at_ks.uiuc.edu]
> > > > Sent: Friday, February 13, 2015 3:55 PM
> > > > To: Norman Geist
> > > > Cc: VMD Mailing List
> > > > Subject: Re: vmd-l: Handful of rendering issues
> > > >
> > > > Norman,
> > > > Please try this experiment for me:
> > > > Set the environment variable VMDOPTIXBUILDER to "MedianBvh"
> > > > and try rendering the same scenes you have been rendering that
> > > > caused trouble. I'm suspicious that you have found some kind
> > > > of bug in the "Trbvh" builder in OptiX 3.6.x, because there were
> > > > a string of buglets that got fixed in "Trbvh" and I wonder if
> > > > there were still a few more hanging out there. Switching to
> > > > "MedianBvh" changes nothing that VMD does, but it changes which
> > > > acceleration structure builder OptiX uses internally, and the
> > > > "MedianBvh", while not as fast as "Trbvh" has been reliable for
> > > > me in VMD for a long time now, and has performed correctly in all
> > > > of the cases where "Trbvh" has broken.
> > > >
> > > > Make sure you get the capitalization of the builder string correct
> > > > or OptiX will ignore it.
> > > >
> > > > Cheers,
> > > > John Stone
> > > > vmd_at_ks.uiuc.edu
> > > >
> > > >
> > > > On Fri, Feb 13, 2015 at 08:42:15AM +0100, Norman Geist wrote:
> > > > > John,
> > > > >
> > > > > the GPU has 2GB of VRAM. Nothing else, except KDE4 is running.
> > > > > Before starting VMD, nvidia-smi shows 158MB out of 2047MB used.
> > > > > After starting VMD, nvidia-smi shows 282MB out of 2047MB used.
> > > > >
> > > > > So rendering only the ruler then breaks the renderer. My 1st
> > guess
> > > > was that
> > > > > the "empty" ruler molecule
> > > > > having only drawn objects, doesn't have the expected molecule
> > memory
> > > > > structure set up which TachyonOptix tries to
> > > > > transfer to the GPU. Therefore I tried the following, which will
> > lead
> > > > to the
> > > > > same error:
> > > > >
> > > > > 1. open fresh vmd
> > > > > 2. disable axis
> > > > > 3. mol new
> > > > > 4. graphics 0 sphere {1 1 1}
> > > > > 5. render using tachyonoptix
> > > > >
> > > > > Let me know if I can help to dig it down further.
> > > > >
> > > > > Norman Geist.
> > > > >
> > > > > > -----Original Message-----
> > > > > > From: John Stone [mailto:johns_at_ks.uiuc.edu]
> > > > > > Sent: Thursday, February 12, 2015 4:16 PM
> > > > > > To: Norman Geist
> > > > > > Cc: VMD Mailing List
> > > > > > Subject: Re: vmd-l: Handful of rendering issues
> > > > > >
> > > > > > Norman,
> > > > > > How much video memory does your GPU have?
> > > > > > What else are you running on the machine at the time that this
> > > > > > error occurs? (for example, is Google Chrome running? Other
> > > > > > instances of VMD? Anything else that uses the GPU at all?)
> > > > > >
> > > > > > Cheers,
> > > > > > John
> > > > > >
> > > > > > On Thu, Feb 12, 2015 at 09:44:34AM +0100, Norman Geist wrote:
> > > > > > > Hey John,
> > > > > > >
> > > > > > > the exact error message is:
> > > > > > >
> > > > > > > ERROR) OptiXRenderer) ERROR: Unknown error (Details: Function
> > > > > > "RTresult
> > > > > > > _rtContextLaunch2D(RTcontext, unsigned int, RTsize, RTsize)"
> > > > caught
> > > > > > > exception: (bvhtools error)An unexpected memory allocation
> > error
> > > > > > occurred in
> > > > > > > TrivialThrustAllocator, [21823538], [15270173])
> > > > (OptiXRenderer.C:1188
> > > > > > >
> > > > > > > GPU is a Geforce GTX660 (propritary NVidia driver version:
> > > > 343.22)
> > > > > > >
> > > > > > > This error occurs for me doing the following steps:
> > > > > > >
> > > > > > > 1. open a fresh vmd
> > > > > > > 2. disable axis
> > > > > > > 3. enable ruler in scale mode
> > > > > > > 4. render using TachyonOptix (interactive or not)
> > > > > > >
> > > > > > > Norman Geist.
> > > > > > >
> > > > > > > > -----Original Message-----
> > > > > > > > From: John Stone [mailto:johns_at_ks.uiuc.edu]
> > > > > > > > Sent: Wednesday, February 11, 2015 5:21 PM
> > > > > > > > To: Norman Geist
> > > > > > > > Cc: 'Tristan Croll'; VMD Mailing List
> > > > > > > > Subject: Re: vmd-l: Handful of rendering issues
> > > > > > > >
> > > > > > > > Norman,
> > > > > > > >
> > > > > > > > On Wed, Feb 11, 2015 at 04:32:35PM +0100, Norman Geist
> > wrote:
> > > > > > > > > 1. Using the "ruler" in "scale" mode, when
> > nothing
> > > > else
> > > > > > > > (including
> > > > > > > > > axis) is visible, TachyonOptix will crash.
> > > > > > > >
> > > > > > > > I don't get a crash when I do this on my system here, but I
> > > > will
> > > > > > > > say that the rendering of the scale bar is pretty wacky due
> > to
> > > > > > > > weaknesses in the scheme I used for setting cylinder radii
> > for
> > > > > > OptiX
> > > > > > > > when drawing lines in VMD 1.9.2, something that still needs
> > > > more
> > > > > > work.
> > > > > > > > Can you post the error message that VMD prints?
> > > > > > > > Without the error it's hard to say what's going on there
> > for
> > > > you.
> > > > > > > >
> > > > > > > > > 2. The general fact TachyonOptix will no more
> > work
> > > > > > without
> > > > > > > > > restarting VMD, if it has crashed once.
> > > > > > > >
> > > > > > > > It depends. If the OptiX runtime runs out of GPU memory or
> > > > other
> > > > > > > > scenarios that it can't bail out of, it will terminate
> > > > rendering
> > > > > > and
> > > > > > > > usually destroy the OptiX context on its way down. In some
> > of
> > > > > > these
> > > > > > > > cases,
> > > > > > > > the state of the CUDA context also gets destroyed, and VMD
> > is
> > > > not
> > > > > > able
> > > > > > > > to
> > > > > > > > recover it. There are also a lot of cases where VMD does
> > > > recover
> > > > > > from
> > > > > > > > less serious issues, but unfortunately, I'd say that
> > running
> > > > the
> > > > > > GPU
> > > > > > > > out
> > > > > > > > of memory is one of the more common problems, particularly
> > on a
> > > > > > machine
> > > > > > > > where other graphical apps are competing for resources
> > (e.g.
> > > > Google
> > > > > > > > Chrome,
> > > > > > > > a surprisingly resource hungry application, in terms of GPU
> > > > > > memory...)
> > > > > > > >
> > > > > > > > Cheers,
> > > > > > > > John
> > > > > > > >
> > > > > > > >
> > > > > > > > > Norman Geist.
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-
> > > > l_at_ks.uiuc.edu]
> > > > > > On
> > > > > > > > Behalf
> > > > > > > > > Of Tristan Croll
> > > > > > > > > Sent: Wednesday, February 11, 2015 12:15 PM
> > > > > > > > > To: vmd-l_at_ks.uiuc.edu
> > > > > > > > > Subject: vmd-l: Handful of rendering issues
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > Hi there,
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > I have a few minor rendering-related
> > issues/suggestions in
> > > > VMD
> > > > > > > > 1.9.2:
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > - If I have an isosurface visualised in the default
> > point
> > > > > > > > representation
> > > > > > > > > and switch to GLSL rendermode, every point becomes a
> > VERY
> > > > > > large
> > > > > > > > sphere and
> > > > > > > > > the system slows to a crawl.
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > - When a wireframe is rendered in Tachyon the lines
> > are of
> > > > > > course
> > > > > > > > replaced
> > > > > > > > > by thin cylinders. This works out nicely in the CPU-
> > only
> > > > > > Tachyon
> > > > > > > > > (particularly if I use a transparent material,
> > yielding a
> > > > > > nicely
> > > > > > > > > unobtrusive mesh), but the cylinder diameter is much
> > > > larger in
> > > > > > > > > Tachyon-OptiX. Is it possible to shrink this, or is
> > this
> > > > one
> > > > > > of
> > > > > > > > the
> > > > > > > > > trade-offs that allows the renderer to be so blazingly
> > > > fast?
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > - When using the interactive renderer, closing the
> > > > rendering
> > > > > > > > window with
> > > > > > > > > the mouse rather than pressing Esc or q crashes VMD.
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > - I think it would be awesome if the interactive
> > renderer
> > > > had
> > > > > > an
> > > > > > > > option to
> > > > > > > > > render the scene at some multiple of the screen
> > > > resolution,
> > > > > > for
> > > > > > > > when
> > > > > > > > > poster-quality images are needed.
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > Cheers,
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > Tristan
> > > > > > > > >
> > > > > > > > >
> > > > > > > >
> > > > > > > > --
> > > > > > > > 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/
> > > > > >
> > > > > > --
> > > > > > 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/
> > > >
> > > > --
> > > > 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/
> >
> > --
> > 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/ 

-- 
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/