From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Aug 15 2010 - 04:28:42 CDT

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.

> 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?

> 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.

axel
axel.

>
> 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/      Fax: 217-244-6078
>
>
>
> --
> Blog: http://www.edwardpku.com/cun
>

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.