From: Stephen Thomas (stephenthomas1_at_boisestate.edu)
Date: Wed Dec 20 2017 - 10:14:35 CST

Thanks! In my case, the stdout is captured, I think by slurm into out.o as
per my slurm setting in submit.sh.

On Wed, Dec 20, 2017 at 8:50 AM Ashar Malik <asharjm_at_gmail.com> wrote:

> 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
>> <https://maps.google.com/?q=405+N.+Mathews+Ave,+Urbana,+IL+61801&entry=gmail&source=g>
>> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
>> http://www.ks.uiuc.edu/Research/vmd/
>>
>>
>
>
> --
> Best,
> /A
>