VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Dec 20 2013 - 12:38:47 CST

Avisek,
  For starters, just try running it on the login node like this, and
let me know if that works fine as a starting point. This will help
ensure that there aren't any issues with file permissions or the like,
since you're not part of our PRAC team. I believe I left the permissions
open, but let me know if you have any trouble with this first step:
  /u/sciteam/stonej/bin/vmd -dispdev text

Once you get that working, I can tell you how to run parallel MPI jobs,
and visualization/rendering jobs and such if/when that's of interest to you.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Dec 20, 2013 at 12:32:48PM -0600, Avisek Das wrote:
> Hi John,
>
> That's a relief. I am not doing anything fancy, I just want to run some
> analysis scripts. I do not intend to use it for visualization. Please give
> me the path to your installation and instructions for using it on Blue
> Waters.
>
> Thanks a lot,
> Avisek
>
> On Fri, Dec 20, 2013 at 12:11 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> I already have a VMD installation on Blue Waters, so
> there's no need for you to install your own unless you are
> customizing it in some way. My installation also adds support
> for BW-specific capabilities such as MPI, OpenGL off-screen rendering
> via Pbuffers, and GPU-accelerated ray tracing using OptiX.
>
> Are you planning to run VMD solely for analysis, or do you want
> to do visualization on BW as well? The way you run the BW version
> of VMD depends on what you're trying to accomplish. I can give you
> examples if you tell me more about what you want to do with VMD on BW.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Dec 20, 2013 at 11:55:25AM -0600, Avisek Das wrote:
> > Hi,
> >
> > I installed VMD on Blue Waters supercomputer at NCSA. The
> installation
> > went fine but I am having difficulty launching the program (in text
> mode).
> > I kept getting the following error
> >
> > "Unknown colorls variable `mh'."
> >
> > I contacted the support staff but they said that there was nothing
> they
> > could do about it and I should take this up to the developers.
> >
> > Please help me fix this problem.
> >
> > Thanks,
> > Avisek
> --
> 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/ 

-- 
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/