VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon May 07 2018 - 15:46:32 CDT

Hi,

On Mon, May 07, 2018 at 08:44:18PM +0000, Goedde, Chris wrote:
> Thanks very much for the reply.
>
> > You didn't indicate whether or not your Jupyter notebook had redirected
> > the stdin stream to VMD. What happens if you redirect /dev/null into the
> > stdin input of VMD on your machine?
>
> I confess I don???t understand this suggestion. Why would I do that and what would it tell me?

It would help narrow down if VMD is existing because it's getting an EOFon
stdin, or some other similar issue, for example. Or alternately, it might
indicate if there's some strange interaction between the display resize
command and stdin handling. I have seen some oddball things before, so
this is a question intended to narrow down the exact source of your problem.
 
> > Does your Jupyter wrapper terminate
> > the subprocess when any output comes to stderr? I ask because I've seen
> > other people's server-side VMD wrappers run into such problems, where their
> > outer wrapper closes down the child process if any output goes to stderr.
>
> I don???t think so. I changed my test input file so it wrote to stderr and the text appeared in the stderr log file.
>
> > Neither the "display reposition" nor the "display resize" command should result
> > in any errors or other unusual behavior, at least none that I'm aware of,
> > if you're running VMD in text mode.
>
> I wouldn???t have thought so.

See what happens if you redirect stdin...

Best,
  John 

-- 
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/