VMD-L Mailing List

From: Avisek Das (avisekchem_at_gmail.com)
Date: Fri Dec 20 2013 - 13:05:17 CST

Hi John,

You are right. It worked when I renamed .bashrc. So, I guess, whenever I
have to use VMD I have to go through this step, which is okay.

Please send me the additional instructions.

Thanks a lot,
Avisek

On Fri, Dec 20, 2013 at 12:47 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

> 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/
>