From: Cun Zhang (apzc2529_at_gmail.com)
Date: Mon Aug 16 2010 - 04:02:55 CDT

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
>

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Blog: http://www.edwardpku.com/cun