VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Feb 18 2009 - 17:43:14 CST

Hi,
  Yes, I didn't bother with compiling stride/surf/tachyon for this
initial test. I'll make a more complete build for you later on now
that I know that the current version seems to address the problem
you were having.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Feb 18, 2009 at 06:32:26PM -0500, Yinglong Miao wrote:
> 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 

-- 
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