VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Dec 20 2013 - 12:47:52 CST

Avisek,
  I'm betting that this is some alias you have setup in your .bashrc or
.cshrc etc on your BW account. Can you try renaming your .bashrc/.cshrc
temporarily and see if the problem goes away?

Cheers,
  John

On Fri, Dec 20, 2013 at 12:45:45PM -0600, Avisek Das wrote:
> Hi John,
>
> Thanks for sharing this with me. Unfortunately I got the same error
> message.
>
> avisek_at_h2ologin2:~> /u/sciteam/stonej/bin/vmd -dispdev text
> Unknown colorls variable `mh'.
> avisek_at_h2ologin2:~>
>
> Please let me know what to do next.
>
> Thanks,
> Avisek
>
> On Fri, Dec 20, 2013 at 12:38 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> 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/ 

-- 
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/