VMD-L Mailing List

From: Cun Zhang (apzc2529_at_gmail.com)
Date: Sun Aug 15 2010 - 08:01:14 CDT

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