VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 22 2008 - 16:16:15 CDT

Samir,
  VMD can indeed be compiled without the need for X.
The autoconf stuff you're using is not how we normally build VMD,
that must be something that the Portage package maintainer put
together, so I can't really comment on it except to say that it's
undoubtably only capable of handling a tiny subset of the configuration
variations that are possible with our own build system. If you compile
VMD from source code directly using our config system, you can build
it without X/OpenGL at all, in pure text mode.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jul 22, 2008 at 03:52:34PM -0500, Samir Unni wrote:
> Hi,
>
> That worked perfectly! I guess reducing the dimensions of the video really
> makes a difference in the rendering time. I don't think I need anything that
> isn't exported to an external renderer, though I'll let you know if I do
> need that in the future.
>
> However, there is one other issue related to this. Does VMD require X to be
> present on a system for it to compile properly? When I try to manually
> compile the VMD plugins (using the tarball from the VMD site) on a system
> without X, autoconf won't exit without an error. The machine is running
> Gentoo Linux, and when I try to compile VMD using Portage (the package
> manager), by default, it tries to download X as a dependency. I don't see a
> USE flag (used to define compile-time options in Portage) for VMD that would
> allow me to disable X support in VMD (though that may be a shortcoming on
> the part of the package maintainer's ebuild, and not a deficiency in VMD).
> Do you know if there's a way to compile VMD even if X isn't installed on the
> system?
>
> Thanks,
>
> Samir
>
>
> On Tue, Jul 22, 2008 at 1:51 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> >
> >
> > Samir,
> > Please try the attached revised version of the movie maker plugin, along
> > with the test script I've provided. To use this, simply move or rename the
> > "vmdmovie1.6" directory typically found installed in:
> > /usr/local/lib/vmd/plugins/noarch/tcl/vmdmovie1.6
> >
> > I'd suggest to rename it to oldvmdmovie1.6 to make sure it doesn't
> > somehow get in the way of the new one I'm providing for you in this email.
> > Unpack the one I've attached, so it ends up as:
> > /usr/local/lib/vmd/plugins/noarch/tcl/vmdmovie1.7
> >
> > A simple test script to try is attached as well.
> > You'll see that I've got it using the "libtachyon" movie type
> > when running in pure text mode, this should be fast enough in many
> > cases and will work without a display/window system connection.
> >
> > If you need to render something that isn't exported to the external
> > renderers, let me know and I'll see if I can give you a test version
> > that will... :)
> >
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Mon, Jul 21, 2008 at 12:46:17PM -0500, John Stone wrote:
> > >
> > > I'll send you an email later today with some scripts, I'll cover the
> > > other questions you asked regarding Tachyon speed etc at that time as
> > well.
> > >
> > > Cheers,
> > > John
> > >
> > > On Mon, Jul 21, 2008 at 12:22:20PM -0500, Samir Unni wrote:
> > > > Hi,
> > > >
> > > > Does that mean there is a command that I can use in the state file to
> > > > manually require the vmdmovie package so it can be used without X, at
> > least
> > > > until the support for rendering without a GUI is improved? Do you know
> > the
> > > > syntax for including such a command in the state file?
> > > >
> > > > Thanks,
> > > >
> > > > Samir
> > > >
> > > >
> > > > On Mon, Jul 21, 2008 at 12:01 PM, Axel Kohlmeyer <
> > > > akohlmey_at_cmm.chem.upenn.edu> wrote:
> > > >
> > > > > On Mon, 21 Jul 2008, Samir Unni wrote:
> > > > >
> > > > > SU> Hi,
> > > > > SU>
> > > > > SU> Yes, that fixed the problem! Is the state variable that's missing
> > one
> > > > > of 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,
> > > > > since
> > > > > SU> I will be using the state files I'm creating with instances of
> > VMD that
> > > > > are
> > > > > SU> on servers where X is not present. Is there a scriptable
> > workaround for
> > > > > this
> > > > > SU> issue as well?
> > > > >
> > > > > if you are running without a display you have to
> > > > > "require" all packages you want to use.
> > > > > all packages with a GUI (and the ones those depends on)
> > > > > have to be "required" by VMD during startup to be able
> > > > > to register their GUI. if john finds a way to set up the
> > > > > initialization properly, then it should work as well
> > > > > on machines without display, provided you use a renderer
> > > > > different from "snapshot", that is.
> > > > >
> > > > > cheers,
> > > > > axel.
> > > > >
> > > > >
> > > > > 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
> > > > > work
> > > > > SU> > on
> > > > > SU> > > the Mac either. It just briefly opens the video (for one
> > frame, I
> > > > > think)
> > > > > SU> > and
> > > > > SU> > > then closes. I'm using the 1.8.6 version of VMD?is that the
> > one
> > > > > 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>
> > > > > wrote:
> > > > > SU> > >
> > > > > SU> > > > Hi,
> > > > > SU> > > >
> > > > > SU> > > > I tried that, but it didn't work for me. When I attempted
> > to play
> > > > > 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 it
> > > > > SU> > > > again on the Mac at work tomorrow morning and see if it
> > works
> > > > > there.
> > > > > SU> > > > However, this was the exact same problem I was previously
> > having
> > > > > on 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
> > > > > 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>
> > > > > 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
> > > > > the
> > > > > SU> > > >> original vmdmovie plugin and the command I emailed
> > earlier. If
> > > > > that
> > > > > SU> > > >> works for you, then we can proceed with debugging whatever
> > has
> > > > > been
> > > > > SU> > > >> changed in your modified version. Starting with your
> > modified
> > > > > version
> > > > > SU> > > >> is likely to add more confusion so I'd rather leave that
> > for a
> > > > > second
> > > > > SU> > > >> step. Please try the example sequence I sent earlier and
> > let me
> > > > > know
> > > > > SU> > > >> if that works with the unmodified script on your system,
> > or not.
> > > > > SU> > > >>
> > > > > SU> > > >> Cheers,
> > > > > SU> > > >> John Stone
> > > > > SU> > > >> vmd_at_ks.uiuc.edu
> > > > > SU> > > >>
> > > > > SU> > > >> On Thu, Jul 17, 2008 at 09:18:24PM -0500, Samir Unni
> > wrote:
> > > > > SU> > > >> > Hi,
> > > > > SU> > > >> >
> > > > > SU> > > >> > That character resulted from an issue with the email
> > > > > formatting; it
> > > > > SU> > was
> > > > > SU> > > >> not
> > > > > SU> > > >> > actually part of the command that I used. The command I
> > used
> > > > > was:
> > > > > SU> > > >> >
> > > > > SU> > > >> > ::MovieMaker::makemovie /Users/srunni/dev/vmd_tests/1fas
> > 1fas
> > > > > SU> > ppmtompeg
> > > > > SU> > > >> > snapshot 10
> > > > > SU> > > >> >
> > > > > SU> > > >> > Also, I sent an update a few hours after my initial
> > email, but
> > > > > it
> > > > > SU> > seems
> > > > > SU> > > >> not
> > > > > SU> > > >> > to have made it onto the mailing list. I will repost it
> > here:
> > > > > SU> > > >> >
> > > > > SU> > > >> > --------------------
> > > > > SU> > > >> > I've got a small update. I slightly changed
> > vmdmovie.tcl, so
> > > > > that
> > > > > SU> > the
> > > > > SU> > > >> > framerate can be passed to the 'makemovie' method. When
> > I did
> > > > > this,
> > > > > SU> > > >> defined
> > > > > SU> > > >> > 'framerate' as the extra variable being passed now, and
> > > > > defined
> > > > > SU> > > >> 'numframes'
> > > > > SU> > > >> > as the product of the framerate and the duration, a
> > working
> > > > > movie
> > > > > SU> > was
> > > > > SU> > > >> > created. Though it would seem that only 2 of these 3
> > variables
> > > > > need
> > > > > SU> > to
> > > > > SU> > > >> be
> > > > > SU> > > >> > defined for the program to be able to determine the 3rd,
> > when
> > > > > I
> > > > > SU> > > >> eliminated
> > > > > SU> > > >> > any one of them, the movie was not generated correctly.
> > I have
> > > > > SU> > attached
> > > > > SU> > > >> the
> > > > > SU> > > >> > working version of vmdmovie.tcl, if anyone wants to look
> > at
> > > > > it.
> > > > > SU> > > >> >
> > > > > SU> > > >> > I would still like to know if there is a way to generate
> > a
> > > > > movie
> > > > > SU> > from
> > > > > SU> > > >> the
> > > > > SU> > > >> > command line without modifying any files that are a part
> > of
> > > > > VMD, if
> > > > > SU> > > >> > possible.
> > > > > SU> > > >> > --------------------
> > > > > SU> > > >> >
> > > > > SU> > > >> > I still have not found a workaround for this issue. The
> > > > > command I am
> > > > > SU> > > >> using
> > > > > SU> > > >> > now is:
> > > > > SU> > > >> >
> > > > > SU> > > >> > ::MovieMaker::makemovie /Users/srunni/dev/vmd_tests/1fas
> > 1fas
> > > > > SU> > ppmtompeg
> > > > > SU> > > >> > tachyon 5 40
> > > > > SU> > > >> >
> > > > > SU> > > >> > Thanks,
> > > > > SU> > > >> >
> > > > > SU> > > >> > Samir Unni
> > > > > SU> > > >> >
> > > > > SU> > > >> >
> > > > > SU> > > >> > On Thu, Jul 17, 2008 at 5:02 PM, John Stone <
> > > > > johns_at_ks.uiuc.edu>
> > > > > SU> > wrote:
> > > > > SU> > > >> >
> > > > > SU> > > >> > >
> > > > > SU> > > >> > > Hi,
> > > > > SU> > > >> > > The ">" character you have in your example below
> > shouldn't
> > > > > be
> > > > > SU> > there,
> > > > > SU> > > >> > > that would cause some trouble for sure.
> > > > > SU> > > >> > >
> > > > > SU> > > >> > > Here's a proper example command sequence to make a
> > movie
> > > > > from text
> > > > > SU> > > >> mode:
> > > > > SU> > > >> > > package require vmdmovie
> > > > > SU> > > >> > > mkdir /tmp/mytmpdir
> > > > > SU> > > >> > > ::MovieMaker::makemovie /tmp/mytmpdir example
> > ppmtompeg
> > > > > snapshot
> > > > > SU> > 10
> > > > > SU> > > >> > >
> > > > > SU> > > >> > > This worked fine for me.
> > > > > SU> > > >> > >
> > > > > SU> > > >> > > Try that and let me know how it goes.
> > > > > SU> > > >> > >
> > > > > SU> > > >> > > Cheers,
> > > > > SU> > > >> > > John Stone
> > > > > SU> > > >> > > vmd_at_ks.uiuc.edu
> > > > > SU> > > >> > >
> > > > > SU> > > >> > > On Wed, Jul 16, 2008 at 09:32:37AM -0500, Samir Unni
> > wrote:
> > > > > SU> > > >> > > > Hi,
> > > > > SU> > > >> > > >
> > > > > SU> > > >> > > > I'm trying to create a Tcl script that will use
> > output
> > > > > from APBS
> > > > > SU> > to
> > > > > SU> > > >> > > create a
> > > > > SU> > > >> > > > video file, with no user interaction. So far, I have
> > > > > managed to
> > > > > SU> > > >> manually
> > > > > SU> > > >> > > > create a state file, to which I can then add a few
> > lines
> > > > > of code
> > > > > SU> > for
> > > > > SU> > > >> the
> > > > > SU> > > >> > > > Movie Plugin, to automatically generate the video
> > file and
> > > > > then
> > > > > SU> > exit
> > > > > SU> > > >> VMD.
> > > > > SU> > > >> > > > However, I can't seem to get VMD to properly
> > generate the
> > > > > video
> > > > > SU> > file
> > > > > SU> > > >> when
> > > > > SU> > > >> > > I
> > > > > SU> > > >> > > > use the script. It creates a file, but it doesn't
> > seem to
> > > > > SU> > contain
> > > > > SU> > > >> any
> > > > > SU> > > >> > > actual
> > > > > SU> > > >> > > > data (it's only about 20 KB), and doesn't play
> > correctly
> > > > > when I
> > > > > SU> > open
> > > > > SU> > > >> it
> > > > > SU> > > >> > > with
> > > > > SU> > > >> > > > MPlayer. This is the line of code that seems to be
> > the
> > > > > problem:
> > > > > SU> > > >> > > >
> > > > > SU> > > >> > > > ::MovieMaker::makemovie
> > /Users/srunni/dev/vmd_tests/1fas
> > > > > 1fas
> > > > > SU> > > >> ppmtompeg
> > > > > SU> > > >> > > > > snapshot 10
> > > > > SU> > > >> > > >
> > > > > SU> > > >> > > >
> > > > > SU> > > >> > > > When I load this exact same state file, but with
> > that line
> > > > > SU> > removed,
> > > > > SU> > > >> and
> > > > > SU> > > >> > > > manually use the Movie Plugin, there are no
> > problems. I
> > > > > figured
> > > > > SU> > out
> > > > > SU> > > >> the
> > > > > SU> > > >> > > > syntax for the above code by taking a look at
> > > > > vmdmovie.tcl, and
> > > > > SU> > > >> imitating
> > > > > SU> > > >> > > > the calls made when the Movie Plugin is launched
> > from the
> > > > > GUI.
> > > > > SU> > As
> > > > > SU> > > >> far as
> > > > > SU> > > >> > > I
> > > > > SU> > > >> > > > can tell, I have made no mistakes in the syntax.
> > Does
> > > > > anyone
> > > > > SU> > know
> > > > > SU> > > >> why
> > > > > SU> > > >> > > this
> > > > > SU> > > >> > > > isn't working correctly?
> > > > > SU> > > >> > > >
> > > > > SU> > > >> > > > Thanks,
> > > > > SU> > > >> > > >
> > > > > SU> > > >> > > > Samir Unni
> > > > > SU> > > >> > >
> > > > > SU> > > >> > > --
> > > > > SU> > > >> > > NIH Resource for Macromolecular Modeling and
> > Bioinformatics
> > > > > SU> > > >> > > Beckman Institute for Advanced Science and Technology
> > > > > SU> > > >> > > University of Illinois, 405 N. Mathews Ave, Urbana, IL
> > 61801
> > > > > SU> > > >> > > Email: johns_at_ks.uiuc.edu Phone:
> > > > > 217-244-3349
> > > > > SU> > > >> > > WWW: http://www.ks.uiuc.edu/~johns/>
> > <http://www.ks.uiuc.edu/%7Ejohns/>
> > > > > <http://www.ks.uiuc.edu/%7Ejohns/>
> > > > > SU> > <http://www.ks.uiuc.edu/%7Ejohns/><
> > > > > SU> > > >> http://www.ks.uiuc.edu/%7Ejohns/>
> > > > > SU> > > >> > > Fax: 217-244-6078
> > > > > SU> > > >> > >
> > > > > SU> > > >>
> > > > > SU> > > >> --
> > > > > SU> > > >> NIH Resource for Macromolecular Modeling and
> > Bioinformatics
> > > > > SU> > > >> Beckman Institute for Advanced Science and Technology
> > > > > SU> > > >> University of Illinois, 405 N. Mathews Ave, Urbana, IL
> > 61801
> > > > > SU> > > >> Email: johns_at_ks.uiuc.edu Phone:
> > 217-244-3349
> > > > > SU> > > >> WWW: http://www.ks.uiuc.edu/~johns/>
> > <http://www.ks.uiuc.edu/%7Ejohns/>
> > > > > <http://www.ks.uiuc.edu/%7Ejohns/><
> > > > > SU> > http://www.ks.uiuc.edu/%7Ejohns/>
> > > > > SU> > > >> Fax: 217-244-6078
> > > > > SU> > > >>
> > > > > SU> > > >
> > > > > SU> > > >
> > > > > SU> >
> > > > > SU> > --
> > > > > SU> > NIH Resource for Macromolecular Modeling and Bioinformatics
> > > > > SU> > Beckman Institute for Advanced Science and Technology
> > > > > SU> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > > > > SU> > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > > > > SU> > WWW: http://www.ks.uiuc.edu/~johns/>
> > <http://www.ks.uiuc.edu/%7Ejohns/><
> > > > > http://www.ks.uiuc.edu/%7Ejohns/>
> > > > > SU> > Fax: 217-244-6078
> > > > > SU> >
> > > > > SU>
> > > > >
> > > > > --
> > > > >
> > =======================================================================
> > > > > Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu
> > http://www.cmm.upenn.edu
> > > > > Center for Molecular Modeling -- University of Pennsylvania
> > > > > Department of Chemistry, 231 S.34th Street, Philadelphia, PA
> > 19104-6323
> > > > > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel:
> > 1-215-898-5425
> > > > >
> > =======================================================================
> > > > > If you make something idiot-proof, the universe creates a better
> > idiot.
> > > > >
> > >
> > > --
> > > NIH Resource for Macromolecular Modeling and Bioinformatics
> > > Beckman Institute for Advanced Science and Technology
> > > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > > WWW: http://www.ks.uiuc.edu/~johns/ <http://www.ks.uiuc.edu/%7Ejohns/> Fax: 217-244-6078
> >
> > --
> > NIH Resource for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > WWW: http://www.ks.uiuc.edu/~johns/ <http://www.ks.uiuc.edu/%7Ejohns/>
> > Fax: 217-244-6078
> > 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078