VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Nov 06 2003 - 19:26:27 CST

Ioana,
  The first command you listed below is wrong, you can't do both > and |&,
you can only do one or the other. :)

On the second one, I'm willing to be that your zc15Ef.vmd has problems
in that it is blasting right through your script without waiting for things
like files to load. What is in your script?

Thanks,
  John

On Thu, Nov 06, 2003 at 05:19:30PM -0800, Ioana Cozmuta wrote:
> Hi John,
>
> I've tried lots of combinations from that web site including the one you
> suggested, none of them works for this script
>
> If I use
> vmd -dispdev text -eofexit < zc15Ef.vmd> |& tee zc15Ef.out &
> I get the error
> Missing name for redirect
> and I get in the output file the results for the first two steps of the
> calculation only.
> If I use the
> vmd -dispdev text -eofexit < zc15Ef.vmd> zc15Ef.out &
> I get no output at all in the output file.
>
> I've tried this at the unix prompter and in a pbs script and it does not
> work. The only way it works is if at the unix prompter I use
> vmd -dispdev text -e input.file |& output.file
>
> it's the only way I can get the data in an output file but vmd is not
> running in batch mode...
>
> Thanks,
> Ioana
>
> On Thu, 6 Nov 2003, John Stone wrote:
>
> >
> > Ioana,
> > You need to redirect the input to VMD in order to run jobs
> > like that in the background, otherwise the first time that VMD
> > wants input, the background job will freeze waiting for console
> > input. Probably the best way to do this is with a command structure
> > like this:
> > vmd -dispdev text -eofexit < zc15Ef.vmd |& tee zc15Ef.out &
> > or something like
> > vmd -dispdev text -eofexit < input.tcl > output.log &
> >
> > VMD will exit when it hits EOF (end of file) on input in this case.
> >
> > This is mentioned on the command line options documentation page,
> > but perhaps it deserves more text?
> > http://www.ks.uiuc.edu/Research/vmd/current/ug/node189.html
> >
> > Thanks,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Thu, Nov 06, 2003 at 01:46:19PM -0800, Ioana Cozmuta wrote:
> > > Hi,
> > >
> > > I am trying to run vmd in batch mode. The scripts runs fine if I
> > > just
> > > use the following command:
> > >
> > > vmd -dispdev text -e zc15Ef.vmd |& tee zc15Ef.out
> > >
> > > but stops after a few steps if I use
> > > vmd -dispdev text -e zc15Ef.vmd |& tee zc15Ef.out &
> > > or put the command into a pbs script.
> > >
> > > I would appreciate your help/suggestions.
> > > Thanks,
> > > Ioana
> >
> > --
> > 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
> > 

-- 
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