VMD-L Mailing List

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Sep 03 2021 - 05:53:07 CDT

Tachyon sometimes results in speckled surfaces if you have duplicate
representations for that region. It may not be seen in the normal VMD view,
but will show with the rendered version.

On Thu, Sep 2, 2021, 6:18 PM Jason Hlozek <jason.hlozek_at_live.co.za> wrote:

> Ah I think Axel did get it right. I can render using the internal Tachyon
> (as well as TachyonL OptiX/OSPRay) on the 64 bit VMD and not 32 bit.
>
> However, is the non-internal 64-bit Tachyon built into the VMD 1.9.4
> install location? Both the a54 and a51 versions attempt and fail to call
> 'tachyon_WIN64.exe' and I don't see it in the installed directory.
> The internal Tachyon seems to render VDW waters as very speckled instead
> of smooth.
>
> Thanks for the help and insight.
>
> Kind regards
> Jason
>
> ------------------------------
> *From:* John Stone <johns_at_ks.uiuc.edu>
> *Sent:* Thursday, 02 September 2021 18:33
> *To:* Axel Kohlmeyer <akohlmey_at_gmail.com>
> *Cc:* Jason Hlozek <jason.hlozek_at_live.co.za>; vmd-l_at_ks.uiuc.edu <
> vmd-l_at_ks.uiuc.edu>
> *Subject:* Re: vmd-l: Tachyon not rendering large scenes
>
> Hi,
> Given that you're running the older 32-bit VMD, I suspect Axel is
> exactly right. I would suggest that you consider installing the new
> 64-bit VMD 1.9.4 test build and see if that cures your problem.
>
> Best,
> John
>
> On Thu, Sep 02, 2021 at 12:06:30PM -0400, Axel Kohlmeyer wrote:
> > The free 7GB do not matter since you are using 32-bit executables and
> they
> > are limited in how much memory they can address.
> > On Thu, Sep 2, 2021 at 12:03 PM Jason Hlozek <[1]
> jason.hlozek_at_live.co.za>
> > wrote:
> >
> > Hi John
> > The conventional Snapshot OpenGL render does produce the correct
> > '.bmp'.Â
> > Re system resources for Tachyon, the GPU is not engaged at all and
> RAM
> > usage increases by 2GBs but there's still 7GBs of free head room by
> the
> > time Tachyon aborts.Â
> > The external '.dat' scene file is 422MBs and seems to consist
> > predominantly of 3D coordinates so it seems like the grid you
> reference
> > is at least partially built?
> > Kind regards
> > Jason
> >
> >
> --------------------------------------------------------------------------
> >
> > From: John Stone <[2]johns_at_ks.uiuc.edu>
> > Sent: Thursday, 02 September 2021 15:43
> > To: Jason Hlozek <[3]jason.hlozek_at_live.co.za>
> > Cc: [4]vmd-l_at_ks.uiuc.edu <[5]vmd-l_at_ks.uiuc.edu>
> > Subject: Re: vmd-l: Tachyon not rendering large scenes
> > Â
> > Have you checked to ensure that you're not running your system out
> of
> > memory? Do you have a conventional OpenGL rendering of the scene
> in
> > question for comparison? When you render the scene to an external
> > file,
> > how large is the scene file? I notice that in the output you
> included
> > below, there's no console output indicating that spatial
> acceleration
> > grid
> > structures were built, despite the fact that you have the +V flag
> > enabled.
> > That is one of the reasons I'm wondering about the memory exhaustion
> > issue. Another possibility is a runaway grid build of some sort,
> but
> > I haven't seen a problem like that for a very long time, so the odds
> > are somewhat against it.
> >
> > Best,
> > Â John Stone
> > Â [6]vmd_at_ks.uiuc.edu
> >
> > On Thu, Sep 02, 2021 at 12:29:11PM +0000, Jason Hlozek wrote:
> > >Â Â Â Hi
> > >Â Â Â I'm trying to render an overlaid view of multiple ligands
> in the
> > same
> > >Â Â Â protein pocket (i.e. a very busy scene).
> > >Â Â Â If I go above 2-3 protein/ligand pairs in the scene, then
> VMD
> > still writes
> > >Â Â Â the scene file and calls Tachyon as usual but after a few
> > seconds of
> > >Â Â Â processing, instead of proceeding to the completion % bar,
> > Tachyon instead
> > >Â Â Â just ends with VMD saying the render is complete even
> though it
> > didn't
> > >Â Â Â run. The same thing happens if I try to call tachyon from
> the
> > command
> > >Â Â Â line:
> > >Â Â Â "C:\Program Files (x86)\University of Illinois\VMD>
> > .\tachyon_WIN32.exe +V
> > >Â Â Â "C:\Users\user-pc\AppData\Local\VirtualStore\Program Files
> > >Â Â Â (x86)\University of Illinois\VMD\mmpl3_overlay_test"
> > >   Tachyon Parallel/Multiprocessor Ray Tracer  Version
> 0.99.1
> > >   Copyright 1994-2014,   John E. Stone
> > <[7]john.stone_at_gmail.com>
> > >Â Â Â ------------------------------------------------------------
> > >Â Â Â C:\Program Files (x86)\University of Illinois\VMD>"
> > >Â Â Â I thought it might be timing out and tried increasing the
> > windows Timeout
> > >Â Â Â Detection and Recovery (TDR) registry variables as well as
> > disabling them
> > >Â Â Â but it made no difference.
> > >Â Â Â Any suggestions please?
> > >Â Â Â Kind regards
> > >Â Â Â Jason
> >
> > --
> > 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 Â Â Â Â Phone:
> > 217-244-3349
> > [9]http://www.ks.uiuc.edu/Research/vmd/Â Â Â Â Â
> >
> > --
> > Dr. Axel Kohlmeyer  [10]akohlmey_at_gmail.com  [11]https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!pP6qm_XM2E9tpfKTiy8YLz6Lr1XHmi2pEnnvXKINTgRCFIlP70OyhOLqhEcFsOB_VQ$
> <https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!pHrdmIBjl-44ZUSX62jQy1svGMT-P7vhnlpSYAlcI1rOOJCLhI76AgbL1krljKKIXg$>
> > College of Science & Technology, Temple University, Philadelphia PA,
> USA
> > International Centre for Theoretical Physics, Trieste. Italy.
> >
> > References
> >
> > Visible links
> > 1. mailto:jason.hlozek_at_live.co.za <jason.hlozek_at_live.co.za>
> > 2. mailto:johns_at_ks.uiuc.edu <johns_at_ks.uiuc.edu>
> > 3. mailto:jason.hlozek_at_live.co.za <jason.hlozek_at_live.co.za>
> > 4. mailto:vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
> > 5. mailto:vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
> > 6. mailto:vmd_at_ks.uiuc.edu <vmd_at_ks.uiuc.edu>
> > 7. mailto:john.stone_at_gmail.com <john.stone_at_gmail.com>
> > 8. http://www.ks.uiuc.edu/~johns/
> > 9. http://www.ks.uiuc.edu/Research/vmd/
> > 10. mailto:akohlmey_at_gmail.com <akohlmey_at_gmail.com>
> > 11.
> https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!rj4UDi-KzG2GSD5hO09MyAxrj5BSDVzxkpJZHIwlgXP4XNJHGakyU-WSF9s_cVoelQ$
>
> --
> 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/
>