VMD-L Mailing List

From: Cameron Mura (cmura_at_virginia.edu)
Date: Sat May 16 2009 - 18:43:18 CDT

Hi all,

I'm trying to figure out why vmd/python is misbehaving so badly on my
fedora 10 (Python v2.5.2) box... I'm currently trying the pre-built
v1.8.7beta2.bin.LINUXAMD64.opengl binary. The following is typical of
what occurs (I write "typical" because I can get it to misbehave in
other ways, depending on version of VMD (1.8.6-vs-1.8.7), Python
version, values of PYTHONPATH / PYTHONHOME, etc., but this is the
closest to working):
> $] vmd -dispdev text -python
> Info) VMD for LINUXAMD64, version 1.8.7beta2 (May 13, 2009)
> ....snip...
> ....snip...
> Info) Creating CUDA device pool and initializing hardware...
> Info) Starting Python...
> Could not find platform independent libraries <prefix>
> Could not find platform dependent libraries <exec_prefix>
> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>]
> 'import site' failed; use -v for traceback
> Traceback (most recent call last):
> File "<string>", line 1, in <module>
> ValueError: vmdnumpy module not available.
> Info) Text interpreter now Python
> Traceback (most recent call last):
> File "<string>", line 1, in <module>
> File "/usr/local/lib/vmd/scripts/python/Tkinter.py", line 59, in
> <module>
> import _tkinter # If this fails your Python may not be configured
> for Tk
> ImportError: No module named _tkinter
> >>>

I'm particularly perplexed by the Tkinter errors because, outside of
VMD, the following 3-step test works just fine at popping-open a little
Tk widget displaying la cedilla:
> $] python
> Python 2.5.2 (r252:60911, Sep 30 2008, 15:42:03)
> [GCC 4.3.2 20080917 (Red Hat 4.3.2-4)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import _tkinter
> >>> import Tkinter
> >>> Tkinter._test( )
> >>>
Both the system-wide and VMD-provided Tkinter modules are imported fine
into a bare python session:

system-wide:
> $] python -c 'import Tkinter; print Tkinter'
> <module 'Tkinter' from '/usr/lib64/python2.5/lib-tk/Tkinter.pyc'>

VMD's:
> $] setenv PYTHONPATH /usr/local/lib/vmd/scripts/python
> $] python -c 'import Tkinter; print Tkinter'
> <module 'Tkinter' from '/usr/local/lib/vmd/scripts/python/Tkinter.pyc'>
I've looked at "Python modules within VMD"
(http://www.ks.uiuc.edu/Research/vmd/current/ug/node147.html) and
google'd around quite a bit, but still not perfectly clear to me what
could be the culprit here?... (sidenote: the "Could not find platform
dependent(/independent)..." errors above can be overcome by defining
PYTHONHOME as /usr/lib64 and PYTHONPATH as
/usr/lib64/python2.5/site-packages:/some/place/else/:/blah/blah" in
~/.vmdrc, but the vmdnumpy and tkinter problems persist...) fwiw, I have
v24.2 of Numeric installed in a more-or-less standard manner.

Any advice or thoughts on this would definitely be appreciated...

thanks,
cam