VMD-L Mailing List

From: Michael Robinson (michael.robinson1_at_monash.edu)
Date: Sat Jul 25 2020 - 00:00:54 CDT

Hi John,

Miro provided the script that they used in their testing. It's just a short
.tcl script (see below), but when submitting it as a job (instead of just
using vmd -dispdev text -e test.tcl) on both SLURM and PBS based HPC, it
does immediately exit instead of providing the normal output.

The contents of the testing script test.tcl are:

axes location off
> display depthcue off
> display resize 640 720
> for {set i 0} {$i < 20} {incr i} {
> puts $i
> }
> display get size

When executing this in a normal terminal environment with vmd -dispdev text
-e test.tcl, the relevant parts of the output are:

OptiXRenderer) ERROR: Failed to load the OptiX shared library.
> OptiXRenderer) NVIDIA driver may be too old.
> OptiXRenderer) Check/update NVIDIA driver
> Info) Dynamically loaded 3 plugins in directory:
> Info) /usr/local/vmd/1.9.4/lib/plugins/LINUXAMD64/molfile
> after#0
> vmd > 0

1
> 2
> 3
> ...
> 18
> 19
> 640 720

Whereas running the same script within a PBS or SLURM, the output is as
follows:

Info) /usr/local/vmd/1.9.4/lib/plugins/LINUXAMD64/molfile
> after#0
> OptiXRenderer) ERROR: Failed to load the OptiX shared library.
> OptiXRenderer) NVIDIA driver may be too old.
> OptiXRenderer) Check/update NVIDIA driver
> Info) VMD for LINUXAMD64, version 1.9.4a31 (March 13, 2019)
> Info) Exiting normally.

I don't think the exiting is due to the OptiX library - the same message
occurs in the successful output. Given this occurs on completely
independent HPC, it does seem like it may be something to do with the
interaction between a scheduled job and VMD.

Regards,
Michael Robinson

On Sat, 25 Jul 2020 at 04:33, John Stone <johns_at_ks.uiuc.edu> wrote:

> Hi,
> If someone manages to find a reproducible way to cause this to happen,
> let me know, otherwise I will chalk it up as a window manager or video
> driver issue that may be unique to that specific system.
>
> Best regards,
> John Stone
>
> On Fri, Jul 24, 2020 at 12:56:31PM +1000, Michael Robinson wrote:
> > Hi Miro,
> > I've just checked on Gadi, and I could use the 'display resize'
> commands
> > without VMD exiting, and the resizing occurred as appropriate. This is
> > with a completely fresh version of VMD - perhaps you've got some
> settings
> > that are causing issues. You might be able to try making a backup of
> your
> > .vmdrc, and then changing the settings there/resetting it.
> > Kind regards,
> > Michael Robinson
> > On Fri, 24 Jul 2020 at 11:37, Miro Astore <[1]miro.astore_at_gmail.com>
> > wrote:
> >
> > Hi,
> > I am trying to render some movies using scripts on my cluster and
> I'm
> > noticing vmd exits when run
> > display resize
> > This seems rather odd to me, no error messages are printed. Any one
> > interested in helping me debug this?
> >
> > System is nci gadi but I'm not sure what technical details would be
> > relevant.
> > Best, Miro
> > --
> > Miro A. Astore  (he/him)
> > PhD Candidate | Computational Biophysics
> > Office 434 A28 School of Physics
> > University of Sydney
> >
> > References
> >
> > Visible links
> > 1. mailto:miro.astore_at_gmail.com
>
> --
> 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/
>