VMD-L Mailing List

From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Wed Dec 07 2011 - 10:58:01 CST

On Wednesday 07 December 2011 15:26:42 David Cohen-Tanugi wrote:
> Hi Bjoern,
>
> Thank you for the advice! I look forward to trying it.
>
> One quick question, though: Isn't each POVRay file several MB large? So
> does this require uploading thousands of MB-large files onto the cluster?
>
Well, why not run the entire VMD process on the cluster?
You could script your way trough.

Prepare a VMD-Visualization-State file on your workstation, save it, copy it
to the cluster, adjust the path in the vmd state file.

Now write a script a little tcl script which you feed into VMD (just append
stuff to the vmd state file) where you iterate over the frames and "render"
each frame to a pov file (don't forget to remove povray from ${PATH} or give a
wrong path or name).

set nf [molinfo top get numframes]
# Mind the line break after -I
for {set i 0} {$i < $nf} {incr i} {
  render POV3 vmdscene${i}.pov "/usr/bin/povray_" +W1280 +H1024 -I \
  vmdscene${i}.pov -O vmdscene${i}.png +D +X +A +FN +UA
}

I think you get the idea from there.

Cheers,
Bjoern

> Yours,
> David
>
> On Mon, Dec 5, 2011 at 1:46 AM, Bjoern Olausson
<namdlist_at_googlemail.com>wrote:
> > On Monday 05 December 2011 04:35:40 you wrote:
> > > Dear All,
> > >
> > > What are the most effective ways of rendering high-quality and long
> >
> > movies
> >
> > > from VMD trajectories?
> > >
> > > I have been using VMD to visualize long (1000+ frames) trajectories of
> > > molecular dynamics simulations from LAMMPS, and I haven't yet found an
> > > efficient way to render these trajectories into high-quality videos. My
> > > Macbook Pro is quick enough for most purposes but at 2-3 minutes per
> >
> > frame
> >
> > > in Tachyon Internal with ambient occlusion, it seems much more logical
> > > to export the job to a parallel cluster on many nodes.
> > >
> > > In that context, what is the most straightforward and efficient way to
> > > render and encode a very long, high-quality movie from a VMD session?
> > > Strategies that leverage parallelized cluster computing would be
> > > greatly appreciated!
> >
> > Save the scene in the Povray format. To do this quickly, either minimize
> > the
> > windows so that the rendering is really fast, or trick VMD so that it
> > does not
> > find the path to Povray, then it will write the POV-Files, but fails to
> > render
> > them. Once you have all the POV files, adjust the rendering size in the
> > POV files (can easily be done with sed) and render the scene with Povray
> > on a cluster. Now you can use tool of your choice to compile a movie
> > from the images (something like "mencoder")
> >
> > mencoder "mf://*.png" -mf w=800:h=600:fps=15:type=png -ovc xvid
> > -xvidencopts
> >
> > hq_ac:quant_type=mpeg:vhq=4:chroma_opt:bitrate=10000:bf_threshold=-150:as
> > pect=4/3 -o 15fps_xvid.avi
> >
> > Cheers,
> > Bjoern
> >
> >
> > --
> > Bjoern Olausson
> > Martin-Luther-Universität Halle-Wittenberg
> > Institut für Pharmazie
> > Wolfgang-Langenbeck-Str.4
> > 06120 Halle/Saale
> >
> > Phone: +49-345-55-25122 

-- 
Bjoern Olausson
Martin-Luther-Universität Halle-Wittenberg 
Institut für Pharmazie
Wolfgang-Langenbeck-Str.4
06120 Halle/Saale
Phone: +49-345-55-25122