From: Yinglong Miao (yimiao_at_indiana.edu)
Date: Wed Feb 18 2009 - 17:32:26 CST

Hi, John,

I tested the new build and it's great that the warning messages don't show
up any more. Though I copied the "vmd-1.8.7a51/LINUXPPC64" you built for
running, following errors came up during my installation:

~/vmd/vmd-1.8.7a51 -> ./configure LINUX IMD SILENT TCL PTHREADS ACTC
LIBTACHYON NETCDF
~/vmd/vmd-1.8.7a51 -> cd src/
~/vmd/vmd-1.8.7a51/src -> make install
cp: cannot stat `../LINUX/vmd_LINUX': No such file or directory
cp: cannot stat `../lib/stride/stride_LINUX': No such file or directory
cp: cannot stat `../lib/surf/surf_LINUX': No such file or directory
cp: cannot stat `../lib/tachyon/tachyon_LINUX': No such file or directory
Make sure /N/u/yimiao/BigRed/bin/vmd7 is in your path.
VMD installation complete. Enjoy!

You can ceratinly fix it for future distribution. Thanks for your help!

cheers,
Yinglong

On Wed, Feb 18, 2009 at 10:44 AM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> Hi,
> Please try the test build I've posted for you on BigRed here:
> /N/u/tg-johns/BigRed/vmd/distrib/vmd-1.8.7a51.bin.LINUXPPC64.text.tar.gz
>
> You can install the test build in your own home directory and give it
> a spin. Let me know if you encounter any of those glibc warnings running
> the new test version.
>
> 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