From: Ashar Malik (asharjm_at_gmail.com)
Date: Wed Dec 20 2017 - 09:50:11 CST

Add to what John just said, clusters do not allow for STDOUT -- well at
least in the cases I have seen.
It has to do with how its setup and not necessarily related to VMD.

You could redirect all the output of your script to a log file.

vmd -dispdev text -eofexit < run.tcl > vmd.log

This would redirect things to the log instead of them ending in a black
hole (/dev/null)

On Thu, Dec 21, 2017 at 4:08 AM, John Stone <johns_at_ks.uiuc.edu> wrote:

> Most likely when you're running in your queueing system, it has no
> input terminal. If you're running in such a scenario, you may instead
> want to redirect your input to read from your script, and add the flag
> -eofexit, e.g. like this:
> vmd -dispdev text -eofexit < file.tcl
>
> See:
> http://www.ks.uiuc.edu/Research/vmd/vmd-1.9.3/ug/node246.html
>
> More examples are here:
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/14705.html
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/8600.html
>
> Best,
> John
>
> On Tue, Dec 19, 2017 at 10:55:17PM -0700, Stephen Thomas wrote:
> > Hi,
> >
> > I am unable to run a tcl from vmd using the -e option. However, this
> works
> > fine if I just run the command directly from bash. Here is a minimal
> > example to reproduce the problem.
> >
> > Steps to reproduce:
> > 1) run submit.sh
> > 2) notice that the output does not contain the text "Running tcl
> script"
> > as seen in run.tcl
> >
> > Can anyone suggest what I might be doing wrong?
> >
> > Thanks,
> > Stephen Thomas.
>
>
>
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>
>

-- 
Best,
/A