VMD-L Mailing List

From: Cun Zhang (apzc2529_at_gmail.com)
Date: Sun Aug 15 2010 - 03:16:45 CDT

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.

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
2.6.6rc1+
When I compile vmd without LIBTACHYON option, It fails with "Segmentation
fault" when I import vmd module into python.

Thank you!

Cun Zhang

More information is as following:

cunzhang_at_Debian:~$ ipython
Python 2.6.6rc1+ (r266rc1:83691, Aug 5 2010, 17:07:04)
Type "copyright", "credits" or "license" for more information.

IPython 0.10 -- An enhanced Interactive Python.
? -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help -> Python's own help system.
object? -> Details about 'object'. ?object also works, ?? prints more.

In [1]: import vmd
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)

/home/cunzhang/<ipython console> in <module>()

ImportError: /usr/local/lib/vmd/scripts/python/vmd.so: undefined symbol:
ompi_mpi_byte
cunzhang_at_Debian:~$ ipython
Python 2.6.6rc1+ (r266rc1:83691, Aug 5 2010, 17:07:04)
Type "copyright", "credits" or "license" for more information.

IPython 0.10 -- An enhanced Interactive Python.
? -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help -> Python's own help system.
object? -> Details about 'object'. ?object also works, ?? prints more.

In [1]: import vmd
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)

/home/cunzhang/<ipython console> in <module>()

ImportError: /usr/local/lib/vmd/scripts/python/vmd.so: undefined symbol:
ompi_mpi_byte

unzhang_at_Debian:~$ vmd
Info) VMD for LINUXAMD64, version 1.8.8a18 (August 15, 2010)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 4 CPUs detected.
Info) Free system memory: 2427MB (61%)
Info) Creating CUDA device pool and initializing hardware...
Info) Detected 1 available CUDA accelerator:
Info) [0] GeForce 9600 GSO 12 SM_1.1 @ 1.38 GHz, 511MB RAM, KTO, OIO
Info) OpenGL renderer: GeForce 9600 GSO/PCI/SSE2
Info) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVF)
Info) Full GLSL rendering mode is available.
Info) Textures: 2-D (8192x8192), 3-D (2048x2048x2048), Multitexture (4)
Found 4 plugins or data handlers in directory
    '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile'.
vmd > vmdinfo
vmdinfo: version | versionmsg | authors | arch |
freemem | numcpus | cpuaffinity | numcudadevices |
noderank | nodecount | options | www | wwwhelp
vmd > vmdinfo options
LINUXAMD64 OPENGL FLTK TK ACTC CUDA IMD LIBSBALL XINPUT LIBTACHYON VRPN
NETCDF TCL PYTHON PTHREADS NUMPY SILENT
vmd > gopython
Info) Starting Python...
Info) Text interpreter now Python
>>> from vmd import *
>>> from molecule import *
>>> from atomsel import atomsel

On Sun, Aug 15, 2010 at 12:10 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> Hi,
> You can get the bleeding edge Tachyon code from the VMD alpha
> directory in BioFS:
> http://www.ks.uiuc.edu/Research/vmd/alpha/
>
> Let me know if you still need assistance.
>
> John
>
> On Sat, Aug 14, 2010 at 12:06:19PM +0800, Cun Zhang wrote:
> > hi, John
> > I update vmd code from cvs just now. I found the following error when
> I
> > compile it.
> > I visit your site(http://jedi.ks.uiuc.edu/~johns/raytracer/>),
> but can't
> > find Tachyon 0.98.10+.
> > How can I fix this problem ?
> >
> > Thank you!
> > Cun Zhang
> >
> > Compiling LibTachyonDisplayDevice.C --> LibTachyonDisplayDevice.o
> ...
> > LibTachyonDisplayDevice.C:35:2: error: #error "LibTachyonDisplayDevice
> > requires Tachyon version 0.98.10 or higher."
> > LibTachyonDisplayDevice.C: In member function 'void*
> > LibTachyonDisplayDevice::tex_colormaterial(float*, int)':
> > LibTachyonDisplayDevice.C:889: error: 'RT_TRANS_RASTER3D' was not
> declared
> > in this scope
> > LibTachyonDisplayDevice.C:889: error: 'rt_tex_transmode' was not
> declared
> > in this scope
> > make: *** [LibTachyonDisplayDevice.o] Error 1
> >
> > --
> > 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/ <http://www.ks.uiuc.edu/%7Ejohns/>
> Fax: 217-244-6078
> 

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