From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Aug 16 2010 - 11:08:36 CDT

Cun,
  The issue is that the Tachyon code isn't compiled into the shared
library version of VMD. To get that to work, we would need to teach
the shared library builds of VMD to link against a shared library
version of Tachyon, then it should work ok. I'll have to look at this
and get back to you.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Aug 16, 2010 at 05:02:55PM +0800, Cun Zhang wrote:
> Axel,
> I have solved this problem temporarily by just updating plugins,
> say, I just update the cvs code of plugins, re-make and re-install these
> plugins.
> Then Python works fine with vmd shared libraries(VMD for LINUXAMD64,
> version 1.8.8a7 (August 9, 2010)). lammpstrj works well too.
>
> But this is just a temporarily solution. I still have no idea about why
> VMD shared libraries of the newest cvs version can't work within Python.
>
> Thank you for your help!
>
> Cun Zhang
>
> On Sun, Aug 15, 2010 at 9:01 PM, Cun Zhang <apzc2529_at_gmail.com> wrote:
>
> On Sun, Aug 15, 2010 at 5:28 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> wrote:
>
> On Sun, Aug 15, 2010 at 4:16 AM, Cun Zhang <apzc2529_at_gmail.com> wrote:
> > Axel and John,
> > Thank you for your help! I have downloaded it. VMD have been working
> now.
> > Now I'm trying to compile the python shared library of vmd.
>
> i don't think anybody has tried this for quite a while.
>
> The last version( VMD for LINUXAMD64, version 1.8.8a7 (December 25,
> 2009)) works well.
> I just update to the new cvs version( VMD for LINUXAMD64, version
> 1.8.8a18 (August 15, 2010)), then it failed.
>
>
> > When I try to import vmd module into python, it returns:
> > ImportError: /usr/local/lib/vmd/scripts/python/vmd.so: undefined
> symbol:
> > ompi_mpi_byte
> >
> > I compile tachyon with linux-mpi-64 option. The version of PYthon is
>
> why compile tachyon with mpi??? why not with threading?
>
> Compiling linux-64 or linux-64-thr, Python return "Segmentation fault"
> too.
> Sometimes return "./vmd.so: undefined symbol: rt_tex_transmode"
>
>
> > 2.6.6rc1+
> > When I compile vmd without LIBTACHYON option, It fails with
> "Segmentation
> > fault" when I import vmd module into python.
>
> have you used the SHARED option for configure?
> have all libraries included in vmd.so compiled with -fPIC?
> it would first try to compile vmd with as few options as possible
> and take it from there. if you keep getting segfaults, you'll
> have to use a debugger to track them down.
>
>
> Yes, SHARED is open
> Here is:
> root_at_Debian:/home/cunzhang/
> VMD/vmd# ./configure
> using configure.options: LINUXAMD64 OPENGL FLTK TK ACTC CUDA IMD
> LIBSBALL XINPUT LIBTACHYON VRPN NETCDF TCL PYTHON PTHREADS NUMPY SILENT
> SHARED
>
> Sorry, I know nothing about program debugging. :(
> Cun Zhang
>
> --
> Blog: http://www.edwardpku.com/cun

-- 
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