VMD-L Mailing List

From: Sacerdoti, Federico (Federico.Sacerdoti_at_deshaw.com)
Date: Tue Apr 04 2006 - 11:11:16 CDT

Hi,

I have installed vmd 1.8.3 on our Linux x86_64 (Rocks 4.0 - Centos
4.2/RHEL4 based) systems. I notice that vmd has its own compiled in
version of python, which is an older version than the RHEL4 standard:
vmd:

vmd 1.8.3:

>>> import sys
>>> sys.version
'2.2.2 (#1, Jan 31 2005, 10:19:19) \n[GCC 3.3.3 20040412 (Red Hat Linux
3.3.3-7)]'
>>>

native:

>>> import sys
>>> sys.version
'2.3.4 (#1, Feb 17 2005, 21:01:10) \n[GCC 3.4.3 20041212 (Red Hat
3.4.3-9.EL4)]'
>>>

This of course causes lots of problems. Right off the bat _tkinter
cannot be found, although the native python has no problems with it.

I have installed your precompiled python libraries from

http://www.ks.uiuc.edu/Research/vmd/plugins/pythonlib/

But that does not help with _tkinter, since it does not seem to be
included. Perhaps that is due to this unanswered thread:

http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/5862.html

As for Numeric, if I set the PYTHONPATH to something appropriately
awful:
 export
PYTHONPATH=$PYTHONPATH:[...]/vmd-1.8.3/lib/pylib/lib_LINUXAMD64/lib/pyth
on2.2/site-packages/Numeric
then vmd can find Numeric, but there is still an error:

vmd > gopython
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>]
/usr/lib64/python2.3/os.py:282: Warning: 'yield' will become a reserved
keyword in the future
'import site' failed; use -v for traceback

Numeric Python module _numpy not found; vmdnumpy module not available.
ImportError:
/proj/desrad/opt/Linux-x86_64/vmd-1.8.3/lib/pylib/lib_LINUXAMD64/lib/pyt
hon2.2/site-packages/Numeric/_numpy.so: undefined symbol: _Py_NoneStruct

Info) Text interpreter now Python
Traceback (most recent call last):
  File "<string>", line 1, in ?
  File
"/proj/desrad/opt/Linux-x86_64/vmd-1.8.3/lib/scripts/python/Tkinter.py",
line 59, in ?
    import _tkinter # If this fails your Python may not be configured
for Tk
ImportError: No module named _tkinter
>>>

Was the library compiled incorrectly, or did I do something wrong during
installation?

Thanks,
Federico

D.E. Shaw Research LLC
New York