From: Yinglong Miao (yimiao_at_indiana.edu)
Date: Mon Feb 16 2009 - 12:10:11 CST

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