From: Samir Unni (srunni_at_gmail.com)
Date: Mon Jul 21 2008 - 15:18:22 CDT

Hi,

Using a cluster is certainly an option. I'm currently working on
implementing grid processing functionality in PDB2PQR (
http://pdb2pqr.sourceforge.net/) and APBS (http://apbs.sourceforge.net/)
using the Opal Toolkit (http://opaltoolkit.sourceforge.net). One of the
features supported by an Opal grid is parallel computation (though I have
not tried it yet). However, I would also like a usable non-Opal
implementation.

I could test out the parallel rendering functionality right now, using this
Mac. When I run VMD with the tachyon renderer on this machine, only ~35% of
the processing power of the eight cores is being used during the job. This
seems to be due to only two threads running (even though VMD outputs
"Multithreading available, 8 CPUs detected" on startup), though the numbers
don't add up in that case—perhaps I'm reading Activity Monitor incorrectly.
In any case, is it possible to increase the number of threads that VMD uses?
I don't see any information on that in the manual.

Thanks,

Samir

On Mon, Jul 21, 2008 at 2:13 PM, Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu>
wrote:

> On Mon, 21 Jul 2008, Samir Unni wrote:
>
> SU> Hi,
> SU>
> SU> That could prove problematic. Using the 'snapshot' renderer requires
> only
> SU> about 10 seconds on this machine (octo-core 2.8 GHz Intel Xeon Mac Pro)
> with
> SU> the command I mentioned earlier (using the modified vmdmovie.tcl). But
> the
> SU> the 'tachyon' renderer requires upwards of 7 minutes. Is there no other
> SU> renderer option that could be used without X/OpenGL?
>
> there are several options and there are also ways to speed
> up rendering at the expense of some detail or features.
>
> in case you have a cluster of machines, you could consider
> just rendering parts of the movie (while keeping the frames)
> on different nodes and/or run the renderer in parallel (several,
> including tachyon support this with good parallel efficiency)
> and then build the movie afterwards.
>
> i'm pretty certain that john has some good suggestions as well
> (this is his special area of expertise. ;-) ).
>
> cheers,
> axel.
>
> SU>
> SU> Thanks,
> SU>
> SU> Samir
> SU>
> SU>
> SU> On Mon, Jul 21, 2008 at 11:44 AM, John Stone <johns_at_ks.uiuc.edu>
> wrote:
> SU>
> SU> >
> SU> > Hi,
> SU> > Ok, that's good to know. Yes, it should be possible to use the
> makemovie
> SU> > method in pure text mode, but some state variables will have to be
> changed
> SU> > and you won't be able to use the "snapshot" renderer since there's no
> SU> > OpenGL window to take snapshots from. You'll probably want to try
> using
> SU> > tachyon, I'll send you the necessary script tweaks to get it going
> for you.
> SU> > I'll also be improving the text mode movie generator routine
> SU> > for the next release. :)
> SU> >
> SU> > Cheers,
> SU> > John
> SU> >
> SU> > On Mon, Jul 21, 2008 at 11:35:51AM -0500, Samir Unni wrote:
> SU> > > Hi,
> SU> > >
> SU> > > Yes, that fixed the problem! Is the state variable that's missing
> one of
> SU> > the
> SU> > > two (or both) that I initialized in my modified version of
> vmdmovie.tcl?
> SU> > >
> SU> > > Also, even if this problem is fixed, it seems that the 'makemovie'
> method
> SU> > > cannot be used unless a GUI is running (i.e. starting vmd with
> '-dispdev
> SU> > > none' or '-dispdev text' won't work). That isn't an option in my
> case,
> SU> > since
> SU> > > I will be using the state files I'm creating with instances of VMD
> that
> SU> > are
> SU> > > on servers where X is not present. Is there a scriptable workaround
> for
> SU> > this
> SU> > > issue as well?
> SU> > >
> SU> > > Thanks,
> SU> > >
> SU> > > Samir
> SU> > >
> SU> > >
> SU> > > On Mon, Jul 21, 2008 at 10:31 AM, John Stone <johns_at_ks.uiuc.edu>
> wrote:
> SU> > >
> SU> > > > I think I've reproduced the problem you encountered, try doing
> this
> SU> > > > and see if you get different behavior:
> SU> > > >
> SU> > > > Run the command line script as before, and verify that you get
> SU> > > > the 1 frame movie, as before.
> SU> > > >
> SU> > > > Then, after having done this, try opening the GUI for the movie
> SU> > > > maker, through the Extensions->Visualization->Movie Maker menu.
> SU> > > > Once the window is opened, try running the script at the command
> SU> > > > line again. Let me know if it works correctly for you the second
> SU> > > > time. I believe that the issue here is an internal state
> variable
> SU> > > > that's only being properly initialized when the GUI has been
> opened.
> SU> > > > It will be easy to workaround/fix with one or two extra lines of
> SU> > > > scripting if that's all that's causing your problem.
> SU> > > >
> SU> > > > Cheers,
> SU> > > > John Stone
> SU> > > > vmd_at_ks.uiuc.edu
> SU> > > >
> SU> > > >
> SU> > > > On Mon, Jul 21, 2008 at 07:57:59AM -0500, Samir Unni wrote:
> SU> > > > > Hi,
> SU> > > > >
> SU> > > > > Sorry I'm so late in getting back to you. Anyway, that code
> doesn't
> SU> > work
> SU> > > > on
> SU> > > > > the Mac either. It just briefly opens the video (for one frame,
> I
> SU> > think)
> SU> > > > and
> SU> > > > > then closes. I'm using the 1.8.6 version of VMD?is that the one
> SU> > you're
> SU> > > > > using?
> SU> > > > >
> SU> > > > > Thanks,
> SU> > > > >
> SU> > > > > Samir
> SU> > > > >
> SU> > > > >
> SU> > > > > On Thu, Jul 17, 2008 at 10:19 PM, Samir Unni <srunni_at_gmail.com
> >
> SU> > wrote:
> SU> > > > >
> SU> > > > > > Hi,
> SU> > > > > >
> SU> > > > > > I tried that, but it didn't work for me. When I attempted to
> play
> SU> > the
> SU> > > > video
> SU> > > > > > file with MPlayer, the window appeared for a second and then
> SU> > > > disappeared,
> SU> > > > > > just like before. I think only one frame is being recorded.
> SU> > > > > >
> SU> > > > > > Right now I'm trying this on my Linux machine at home, but
> I'll try
> SU> > it
> SU> > > > > > again on the Mac at work tomorrow morning and see if it works
> SU> > there.
> SU> > > > > > However, this was the exact same problem I was previously
> having on
> SU> > the
> SU> > > > Mac,
> SU> > > > > > so I don't think it will. If it's working for you, it might
> have
> SU> > > > something
> SU> > > > > > to do with the state file I'm using, which I created by
> importing
> SU> > the
> SU> > > > DX
> SU> > > > > > output file from APBS into VMD.
> SU> > > > > >
> SU> > > > > > I had meant to attached the modified version of vmdmovie.tcl
> to the
> SU> > > > last
> SU> > > > > > email; it's attached now, if you want to take a look.
> SU> > > > > >
> SU> > > > > > Thanks,
> SU> > > > > >
> SU> > > > > > Samir
> SU> > > > > >
> SU> > > > > >
> SU> > > > > >
> SU> > > > > > On Thu, Jul 17, 2008 at 9:56 PM, John Stone <
> johns_at_ks.uiuc.edu>
> SU> > wrote:
> SU> > > > > >
> SU> > > > > >>
> SU> > > > > >> Hi,
> SU> > > > > >> I'm not sure how you changed your copy of the vmdmovie.tcl
> file,
> SU> > > > > >> but I'd ask that before we delve any further, that you first
> try
> SU> > the
> SU> > > > > >> original vmdmovie plugin and the command I emailed earlier------=_Part_26293_22489915.1216671503033--