From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Thu Nov 06 2003 - 19:19:30 CST
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
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...
On Thu, 6 Nov 2003, John Stone wrote:
> 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?
> John Stone
> 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
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