VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Feb 16 2009 - 13:14:31 CST

Yinglong,
  To build a VMD from source disabling the graphics interface, you
merely have to disable a few of the options passed to 'configure'.
Here's the 'linux.text' target from the top level VMD makefile,
one can start with that, alter the platform as appropriate and
use the same strategy for basically any case where you want to build
a text-only VMD.

##
## Special Linux build for clustermatic/scyld, or plain text mode usage
##
linux.text:
        ./configure LINUX IMD SILENT TCL PTHREADS ACTC LIBTACHYON NETCDF

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Feb 16, 2009 at 01:10:11PM -0500, Yinglong Miao wrote:
> Thanks, John!
>
> I am looking forward to seeing how the new version works. And by the way,
> can you send me instructions of installing VMD on a cluster like BigRed
> without enabling the graphics interface after you are done? I will greatly
> appreciate it!
>
> cheers,
> Yinglong
>
> On Mon, Feb 16, 2009 at 12:54 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> >
> > Yinglong,
> > That's what I was going to guess, but it's always best to ask :-)
> > Probably the best thing would be for me to install a new test build
> > of VMD 1.8.7 on BigRed and see if the problem still crops up. I found
> > and fixed a couple of small bugs that may be responsible for the problem
> > you're seeing, so the new builds of VMD may cure that warning. I'll have
> > to check to make sure I still have an active account on BigRed. If so I'll
> > try a build this week.
> >
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Mon, Feb 16, 2009 at 12:51:38PM -0500, Yinglong Miao wrote:
> > > Hi John,
> > >
> > > Glad to have you here! It's the one you installed on BigRed cluster at
> > > Indiana University.
> > >
> > > Thanks,
> > > Yinglong
> > >
> > > On Mon, Feb 16, 2009 at 12:43 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
> > >
> > > > Hi,
> > > > What platform are you running on, and which version of VMD is this
> > > > email referring to?
> > > >
> > > > Cheers,
> > > > John Stone
> > > > vmd_at_ks.uiuc.edu
> > > >
> > > > On Mon, Feb 16, 2009 at 12:23:32PM -0500, Yinglong Miao wrote:
> > > > > Dear VMD developers/users,
> > > > >
> > > > > I have been running a VMD script that involves loading PSF/PDB files
> > and
> > > > > writing DCD files for a pretty large system (~3M atoms). The program
> > > > seems
> > > > > to run fine with files processed properly, but error messages like
> > "***
> > > > > glibc detected *** free(): invalid pointer: 0x00000000102a8f28 ***"
> > keep
> > > > > coming up during the program running. I am not sure whether it comes
> > from
> > > > > large system processing or something regarding memory. I looked it up
> > in
> > > > the
> > > > > list archives but found no clue. Has anyone come into such cases?
> > Your
> > > > help
> > > > > will be appreciated!
> > > > >
> > > > > Thanks!
> > > > >
> > > > > --
> > > > > Yinglong Miao
> > > > > Ph.D. Candidate
> > > > > Center for Cell and Virus Theory
> > > > > Chemistry Department, Indiana University
> > > > > 800 E Kirkwood Ave Room C203A, Bloomington, IN 47405
> > > > > Tel: 1-812-856-0981
> > > >
> > > > --
> > > > NIH Resource for Macromolecular Modeling and Bioinformatics
> > > > Beckman Institute for Advanced Science and Technology
> > > > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > > > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > > > WWW: http://www.ks.uiuc.edu/~johns/><
> > http://www.ks.uiuc.edu/%7Ejohns/>
> > > > Fax: 217-244-6078
> > > >
> > >
> > >
> > >
> > > --
> > > Yinglong Miao
> > > Ph.D. Candidate
> > > Center for Cell and Virus Theory
> > > Chemistry Department, Indiana University
> > > 800 E Kirkwood Ave Room C203A, Bloomington, IN 47405
> > > Tel: 1-812-856-0981
> >
> > --
> > NIH Resource for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > WWW: http://www.ks.uiuc.edu/~johns/ <http://www.ks.uiuc.edu/%7Ejohns/>
> > Fax: 217-244-6078
> >
>
>
>
> --
> Yinglong Miao
> Ph.D. Candidate
> Center for Cell and Virus Theory
> Chemistry Department, Indiana University
> 800 E Kirkwood Ave Room C203A, Bloomington, IN 47405
> Tel: 1-812-856-0981 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078