From: Bennion, Brian (
Date: Wed Dec 20 2017 - 10:45:35 CST

The treatment of stdout depends on the job manager. The default for slurm is to print all stdout to a file "slurm-JOBID.out"


From: <> on behalf of Ashar Malik <>
Sent: Wednesday, December 20, 2017 7:50:11 AM
To: John Stone; Stephen Thomas; VMD Mailing List
Subject: Re: vmd-l: tcl script not executed when submitted using a slurm script

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 <<>> 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


More examples are here:


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
> 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           Phone: 217-244-3349<tel:217-244-3349>